llm-wiki-compiler 0.7.0 → 0.9.0

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/utils/constants.ts","../src/utils/claude-settings.ts","../src/utils/provider-guard.ts","../src/sdk/wiki.ts","../src/utils/output.ts","../src/commands/ingest.ts","../src/utils/markdown.ts","../src/utils/source-writer.ts","../src/utils/path-confine.ts","../src/viewer/path-safety.ts","../src/utils/activity-log.ts","../src/ingest/web.ts","../src/ingest/file.ts","../src/ingest/shared.ts","../src/ingest/pdf.ts","../src/ingest/image.ts","../src/providers/anthropic.ts","../src/providers/voyage-embed.ts","../src/ingest/transcript.ts","../src/compiler/index.ts","../src/utils/state.ts","../src/compiler/source-state.ts","../src/compiler/hasher.ts","../src/providers/openai.ts","../src/providers/ollama.ts","../src/providers/minimax.ts","../src/providers/copilot.ts","../src/providers/claude-agent.ts","../src/providers/json-schema-to-zod.ts","../src/utils/provider.ts","../src/utils/llm.ts","../src/utils/lock.ts","../src/utils/output-language.ts","../src/compiler/prompts.ts","../src/schema/types.ts","../src/schema/defaults.ts","../src/schema/loader.ts","../src/schema/helpers.ts","../src/compiler/deps.ts","../src/compiler/orphan.ts","../src/compiler/resolver.ts","../src/compiler/indexgen.ts","../src/compiler/prompt-budget.ts","../src/compiler/obsidian.ts","../src/compiler/provenance.ts","../src/utils/embeddings.ts","../src/utils/retrieval.ts","../src/compiler/candidates.ts","../src/utils/candidate-store.ts","../src/linter/rules.ts","../src/freshness/index.ts","../src/compiler/page-renderer.ts","../src/commands/query.ts","../src/linter/index.ts","../src/viewer/snapshot.ts","../src/wiki/collect.ts","../src/viewer/collect.ts","../src/viewer/graph.ts","../src/project/state.ts","../src/linter/cache.ts","../src/project/recommendations.ts","../src/viewer/search.ts","../src/context/provenance.ts","../src/context/ranking.ts","../src/context/retrieval.ts","../src/context/graph.ts","../src/context/budget.ts","../src/context/types.ts","../src/context/build.ts","../src/commands/export.ts","../src/export/collect.ts","../src/export/provenance.ts","../src/export/project-id.ts","../src/export/json-export.ts","../src/export/graphml.ts","../src/eval/health.ts","../src/eval/citation-coverage.ts","../src/eval/source-path.ts","../src/eval/source-utilization.ts","../src/eval/citation-depth.ts","../src/eval/citation-support.ts","../src/eval/stats.ts","../src/eval/delta.ts","../src/eval/thresholds.ts","../src/eval/index.ts","../src/status/collect.ts","../src/search/retrieval.ts","../src/pages/read.ts","../src/pages/list.ts","../src/sources/store.ts"],"sourcesContent":["/**\n * Shared constants for the llmwiki knowledge compiler.\n * Centralized config values to avoid magic numbers scattered across the codebase.\n */\n\n/** Maximum source file size in characters before truncation. */\nexport const MAX_SOURCE_CHARS = 100_000;\n\n/** Minimum source content length to ingest without a warning. */\nexport const MIN_SOURCE_CHARS = 50;\n\n/**\n * Default character budget for the combined source content sent to the LLM\n * during page generation for a single concept (issue #39).\n *\n * Caps the per-prompt content at ~200,000 chars (~50k tokens). When two or\n * more sources contribute to the same concept and their combined raw size\n * exceeds this budget, each source's slice is proportionally truncated so\n * the prompt fits the model's context window. Without this cap, popular\n * concepts that appear in many overlapping documents reliably blow past\n * the LLM provider's context limit and the compile crashes.\n *\n * Override via the LLMWIKI_PROMPT_BUDGET_CHARS env var when running against\n * larger-context (raise) or smaller-context (lower) models.\n */\nexport const DEFAULT_PROMPT_BUDGET_CHARS = 200_000;\n\n/** Env var that overrides DEFAULT_PROMPT_BUDGET_CHARS at runtime. */\nexport const PROMPT_BUDGET_ENV_VAR = \"LLMWIKI_PROMPT_BUDGET_CHARS\";\n\n/** Number of most relevant wiki pages to load for query context. */\nexport const QUERY_PAGE_LIMIT = 5;\n\n/** Maximum concurrent API calls during page generation. */\nexport const COMPILE_CONCURRENCY = 5;\n\n/** API retry configuration. */\nexport const RETRY_COUNT = 3;\nexport const RETRY_BASE_MS = 1000;\nexport const RETRY_MULTIPLIER = 4;\n\n/** Default provider when LLMWIKI_PROVIDER is not set. */\nexport const DEFAULT_PROVIDER = \"anthropic\";\n\n/** Default model per provider. */\nexport const PROVIDER_MODELS: Record<string, string> = {\n  anthropic: \"claude-sonnet-4-6\",\n  \"claude-agent\": \"claude-sonnet-4-6\",\n  openai: \"gpt-4o\",\n  ollama: \"llama3.1\",\n  minimax: \"MiniMax-M2.7\",\n  copilot: \"gpt-4o\",\n};\n\n/** Default Ollama API base URL. */\nexport const OLLAMA_DEFAULT_HOST = \"http://localhost:11434/v1\";\n\n/** GitHub Copilot API base URL (OpenAI-compatible, requires OAuth token). */\nexport const COPILOT_BASE_URL = \"https://api.githubcopilot.com\";\n\n/**\n * Default request timeout for cloud OpenAI-compatible providers (10 minutes).\n * Matches the OpenAI SDK's own default; called out here so it's explicit.\n */\nexport const OPENAI_DEFAULT_TIMEOUT_MS = 10 * 60 * 1000;\n\n/**\n * Default request timeout for Ollama (30 minutes). Local models on modest\n * hardware can take well over the cloud-provider default for a single\n * compile-time completion. Configurable via LLMWIKI_REQUEST_TIMEOUT_MS or\n * OLLAMA_TIMEOUT_MS env vars.\n */\nexport const OLLAMA_DEFAULT_TIMEOUT_MS = 30 * 60 * 1000;\n\n/** Directory names relative to the project root. */\nexport const SOURCES_DIR = \"sources\";\nexport const CONCEPTS_DIR = \"wiki/concepts\";\nexport const QUERIES_DIR = \"wiki/queries\";\nexport const LLMWIKI_DIR = \".llmwiki\";\nexport const STATE_FILE = \".llmwiki/state.json\";\nexport const LOCK_FILE = \".llmwiki/lock\";\nexport const INDEX_FILE = \"wiki/index.md\";\nexport const MOC_FILE = \"wiki/MOC.md\";\n\n/**\n * Append-only activity journal at the project root, per Karpathy's llm-wiki\n * gist: a chronological record of what happened and when (ingests, compiles,\n * queries, lint passes). Lives at the root rather than under wiki/ because it\n * spans project-level operations — ingest writes before any wiki/ exists.\n */\nexport const LOG_FILE = \"log.md\";\n\n/** Max characters for a single log.md entry description before truncation. */\nexport const LOG_DESCRIPTION_MAX_CHARS = 200;\n\n/**\n * Max number of page wikilinks listed in a single log.md entry detail line.\n * Beyond this the list is truncated with a \"(+N more)\" suffix so a large\n * compile doesn't write a wall of links into the journal.\n */\nexport const LOG_MAX_PAGE_LINKS = 20;\nexport const EMBEDDINGS_FILE = \".llmwiki/embeddings.json\";\nexport const LAST_LINT_FILE = \".llmwiki/last-lint.json\";\n\n/** Supported image file extensions for vision-based ingest. */\nexport const IMAGE_EXTENSIONS = new Set([\".jpg\", \".jpeg\", \".png\", \".gif\", \".webp\"]);\n\n/** Supported transcript file extensions (content-sniff .txt separately). */\nexport const TRANSCRIPT_EXTENSIONS = new Set([\".vtt\", \".srt\"]);\n\n/** Max tokens for image-description completions. */\nexport const IMAGE_DESCRIBE_MAX_TOKENS = 2048;\n\n/** Pending review candidates awaiting approval/rejection. */\nexport const CANDIDATES_DIR = \".llmwiki/candidates\";\n\n/** Rejected review candidates archived for audit (not deleted). */\nexport const CANDIDATES_ARCHIVE_DIR = \".llmwiki/candidates/archive\";\n\n/**\n * Per-source hashes already processed by `rules extract` (rule pipeline). Kept\n * separate from STATE_FILE so rule extraction and concept compilation advance\n * their change-detection cursors independently.\n */\nexport const RULE_STATE_FILE = \".llmwiki/rule-state.json\";\n\n/** Pending rule candidates (rule pipeline) awaiting approve/reject. */\nexport const RULE_CANDIDATES_DIR = \".llmwiki/rule-candidates\";\n\n/** Rejected rule candidates archived for audit (not deleted). */\nexport const RULE_CANDIDATES_ARCHIVE_DIR = \".llmwiki/rule-candidates/archive\";\n\n/** Number of most similar pages to return from embedding-based pre-filter. */\nexport const EMBEDDING_TOP_K = 15;\n\n/** Number of chunk candidates to retain after the semantic-similarity step. */\nexport const CHUNK_TOP_K = 30;\n\n/** Number of chunk candidates to keep after reranking. */\nexport const CHUNK_RERANK_KEEP = 12;\n\n/** Target chunk size in characters; chunks try to land near this length. */\nexport const CHUNK_TARGET_CHARS = 800;\n\n/** Hard upper bound on a single chunk's character length. */\nexport const CHUNK_MAX_CHARS = 1_400;\n\n/** Minimum standalone chunk size; smaller trailing fragments are merged back. */\nexport const CHUNK_MIN_CHARS = 200;\n\n/** Provenance metadata thresholds used by lint rules. */\nexport const LOW_CONFIDENCE_THRESHOLD = 0.5;\nexport const MAX_INFERRED_PARAGRAPHS_WITHOUT_CITATIONS = 2;\n\n/** Embedding model to use per provider. */\nexport const EMBEDDING_MODELS: Record<string, string> = {\n  anthropic: \"voyage-3-lite\",\n  \"claude-agent\": \"voyage-3-lite\",\n  openai: \"text-embedding-3-small\",\n  ollama: \"nomic-embed-text\",\n};\n","/**\n * Claude settings fallback helpers.\n *\n * Provides a narrow, read-only integration with `~/.claude/settings.json`.\n * We only read the `env` object and only extract Anthropic-related values that\n * llmwiki can safely consume. Explicit process env values remain higher priority.\n */\n\nimport { readFileSync } from \"node:fs\";\nimport { homedir } from \"node:os\";\nimport path from \"node:path\";\n\nconst CLAUDE_SETTINGS_PATH_ENV = \"LLMWIKI_CLAUDE_SETTINGS_PATH\";\n\ninterface ClaudeSettingsEnv {\n  ANTHROPIC_API_KEY?: string;\n  ANTHROPIC_AUTH_TOKEN?: string;\n  ANTHROPIC_BASE_URL?: string;\n  ANTHROPIC_MODEL?: string;\n}\n\ninterface AnthropicAuthConfig {\n  apiKey?: string;\n  authToken?: string;\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === \"object\" && value !== null;\n}\n\nfunction normalize(value: unknown): string | undefined {\n  if (typeof value !== \"string\") return undefined;\n  const trimmed = value.trim();\n  return trimmed.length > 0 ? trimmed : undefined;\n}\n\nfunction resolveClaudeSettingsPath(env: NodeJS.ProcessEnv): string {\n  return env[CLAUDE_SETTINGS_PATH_ENV] ?? path.join(homedir(), \".claude\", \"settings.json\");\n}\n\nfunction readClaudeSettingsFile(settingsPath: string): string | undefined {\n  try {\n    return readFileSync(settingsPath, \"utf8\");\n  } catch (err) {\n    if (isRecord(err) && err.code === \"ENOENT\") {\n      return undefined;\n    }\n    const message = err instanceof Error ? err.message : String(err);\n    throw new Error(`Failed to read Claude settings at \"${settingsPath}\": ${message}`);\n  }\n}\n\nexport function readClaudeSettingsEnv(env: NodeJS.ProcessEnv = process.env): ClaudeSettingsEnv | undefined {\n  const settingsPath = resolveClaudeSettingsPath(env);\n  const raw = readClaudeSettingsFile(settingsPath);\n  if (!raw) return undefined;\n\n  let parsed: unknown;\n  try {\n    parsed = JSON.parse(raw);\n  } catch (err) {\n    const message = err instanceof Error ? err.message : String(err);\n    throw new Error(`Failed to parse Claude settings at \"${settingsPath}\": ${message}`);\n  }\n\n  if (!isRecord(parsed) || !isRecord(parsed.env)) {\n    return undefined;\n  }\n\n  const values: ClaudeSettingsEnv = {\n    ANTHROPIC_API_KEY: normalize(parsed.env.ANTHROPIC_API_KEY),\n    ANTHROPIC_AUTH_TOKEN: normalize(parsed.env.ANTHROPIC_AUTH_TOKEN),\n    ANTHROPIC_BASE_URL: normalize(parsed.env.ANTHROPIC_BASE_URL),\n    ANTHROPIC_MODEL: normalize(parsed.env.ANTHROPIC_MODEL),\n  };\n\n  if (!values.ANTHROPIC_API_KEY && !values.ANTHROPIC_AUTH_TOKEN && !values.ANTHROPIC_BASE_URL && !values.ANTHROPIC_MODEL) {\n    return undefined;\n  }\n  return values;\n}\n\nfunction tryReadClaudeSettingsEnv(env: NodeJS.ProcessEnv): ClaudeSettingsEnv | undefined {\n  try {\n    return readClaudeSettingsEnv(env);\n  } catch {\n    return undefined;\n  }\n}\n\nfunction validateAnthropicBaseURL(value: string): string {\n  const normalized = value.trim();\n  try {\n    const parsed = new URL(normalized);\n    if (parsed.protocol !== \"http:\" && parsed.protocol !== \"https:\") {\n      throw new Error(\"Must use http:// or https:// protocol.\");\n    }\n  } catch (err) {\n    const message = err instanceof Error ? err.message : \"Must be a valid http(s) URL.\";\n    throw new Error(`Invalid ANTHROPIC_BASE_URL: \"${normalized}\". ${message}`);\n  }\n  return normalized;\n}\n\nexport function resolveAnthropicAuthFromEnv(env: NodeJS.ProcessEnv = process.env): AnthropicAuthConfig {\n  const explicitApiKey = normalize(env.ANTHROPIC_API_KEY);\n  if (explicitApiKey) return { apiKey: explicitApiKey };\n\n  const explicitAuthToken = normalize(env.ANTHROPIC_AUTH_TOKEN);\n  if (explicitAuthToken) return { authToken: explicitAuthToken };\n\n  const fallback = readClaudeSettingsEnv(env);\n  if (fallback?.ANTHROPIC_API_KEY) return { apiKey: fallback.ANTHROPIC_API_KEY };\n  if (fallback?.ANTHROPIC_AUTH_TOKEN) return { authToken: fallback.ANTHROPIC_AUTH_TOKEN };\n  return {};\n}\n\nexport function resolveAnthropicModelFromEnv(env: NodeJS.ProcessEnv = process.env): string | undefined {\n  const explicitModel = env.LLMWIKI_MODEL;\n  if (explicitModel !== undefined) return explicitModel;\n  return tryReadClaudeSettingsEnv(env)?.ANTHROPIC_MODEL;\n}\n\nexport function resolveAnthropicBaseURLFromEnv(env: NodeJS.ProcessEnv = process.env): string | undefined {\n  const explicitBaseURL = normalize(env.ANTHROPIC_BASE_URL);\n  if (explicitBaseURL) return validateAnthropicBaseURL(explicitBaseURL);\n\n  const fallbackBaseURL = tryReadClaudeSettingsEnv(env)?.ANTHROPIC_BASE_URL;\n  if (!fallbackBaseURL) return undefined;\n  return validateAnthropicBaseURL(fallbackBaseURL);\n}\n","/**\n * Single provider-credential guard shared by every entry point that\n * needs an LLM call (CLI compile/query/watch, MCP tools, the upcoming\n * `quickstart` command).\n *\n * The guard throws on failure instead of calling `process.exit(1)`,\n * which lets every caller decide how to surface the failure:\n *\n *  - CLI verbs catch the throw and print the message + exit 1.\n *  - MCP tools let the throw propagate as a tool error.\n *  - `quickstart` catches the throw and translates it into the\n *    `compile.error = { code: \"provider_unavailable\", ... }` shape\n *    documented in the next-quickstart implementation plan.\n *\n * Error messages mirror the rich CLI form (with `Set it with: export X=...`\n * hints) so the user always sees actionable guidance no matter which\n * surface fired the guard.\n */\n\nimport { DEFAULT_PROVIDER } from \"./constants.js\";\nimport { resolveAnthropicAuthFromEnv } from \"./claude-settings.js\";\n\n/** Thrown when the active provider has no usable credentials. */\nexport class ProviderUnavailableError extends Error {\n  readonly code = \"provider_unavailable\" as const;\n  constructor(readonly provider: string, readonly missing: string[], message: string) {\n    super(message);\n    this.name = \"ProviderUnavailableError\";\n  }\n}\n\n/** Thrown when LLMWIKI_PROVIDER names an unsupported provider. */\nexport class UnknownProviderError extends Error {\n  readonly code = \"unknown_provider\" as const;\n  constructor(readonly provider: string, readonly supported: string[], message: string) {\n    super(message);\n    this.name = \"UnknownProviderError\";\n  }\n}\n\n/** Map of provider name to the env var that satisfies it. Null = no key needed. */\nconst PROVIDER_KEY_VARS: Record<string, string | null> = {\n  anthropic: \"ANTHROPIC_API_KEY\",\n  \"claude-agent\": null,\n  openai: \"OPENAI_API_KEY\",\n  ollama: null,\n  minimax: \"MINIMAX_API_KEY\",\n  copilot: \"GITHUB_TOKEN\",\n};\n\n/**\n * Throw if the active LLM provider is missing credentials.\n * Anthropic accepts either ANTHROPIC_API_KEY or ANTHROPIC_AUTH_TOKEN\n * (resolved through the Claude Code settings fallback chain).\n */\nexport function ensureProviderAvailable(): void {\n  const provider = process.env.LLMWIKI_PROVIDER ?? DEFAULT_PROVIDER;\n\n  if (provider === \"anthropic\") {\n    const auth = resolveAnthropicAuthFromEnv();\n    if (!auth.apiKey && !auth.authToken) {\n      throw new ProviderUnavailableError(\n        \"anthropic\",\n        [\"ANTHROPIC_API_KEY\", \"ANTHROPIC_AUTH_TOKEN\"],\n        `Anthropic credentials are required for the \"anthropic\" provider.\\n` +\n          `  Set one of: export ANTHROPIC_API_KEY=<your-key> OR export ANTHROPIC_AUTH_TOKEN=<your-token>`,\n      );\n    }\n    return;\n  }\n\n  const keyVar = PROVIDER_KEY_VARS[provider];\n  if (keyVar === undefined) {\n    const supported = Object.keys(PROVIDER_KEY_VARS);\n    throw new UnknownProviderError(\n      provider,\n      supported,\n      `Unknown provider \"${provider}\".\\n` + `  Supported: ${supported.join(\", \")}`,\n    );\n  }\n\n  if (keyVar && !process.env[keyVar]) {\n    throw new ProviderUnavailableError(\n      provider,\n      [keyVar],\n      `${keyVar} environment variable is required for the \"${provider}\" provider.\\n` +\n        `  Set it with: export ${keyVar}=<your-key>`,\n    );\n  }\n}\n","/**\n * @file src/sdk/wiki.ts\n * @description In-process SDK facade for llmwiki.\n *\n * `createWiki(options)` returns a `Wiki` object that delegates every\n * method to the SDK-safe core functions built across Tasks 1–9. All\n * methods run silently (no console output) by scoping quiet mode to the\n * async call tree via AsyncLocalStorage, so concurrent calls are fully\n * isolated — no global flag is mutated, eliminating the concurrency caveat\n * described in earlier design drafts.\n *\n * Provider-gating rules:\n *   - `compile`, `search`, `query` — always guard (throw ProviderUnavailableError if no creds)\n *   - `runEval({ mode: \"full\" })` — guards only when mode is \"full\"\n *   - All other methods — no credential check; safe to call without an LLM provider\n *\n * Root-path validation: `createWiki` normalizes the root once via `path.resolve`.\n * A non-existent root is accepted — `ingest`/`ingestText` create `sources/` via\n * recursive `mkdir` on first write. If the path already exists but is NOT a\n * directory (e.g. a regular file was passed by mistake), construction throws\n * immediately with a clear error message.\n */\n\nimport path from \"node:path\";\nimport { existsSync, statSync } from \"node:fs\";\nimport { withQuiet } from \"../utils/output.js\";\nimport { ingestSource, ingestTextSource } from \"../commands/ingest.js\";\nimport { compileAndReport } from \"../compiler/index.js\";\nimport { generateAnswer } from \"../commands/query.js\";\nimport { lint } from \"../linter/index.js\";\nimport { buildContextPack } from \"../context/build.js\";\nimport { exportJson } from \"../commands/export.js\";\nimport { runEval, DEFAULT_SAMPLE_SIZE } from \"../eval/index.js\";\nimport { ensureProviderAvailable } from \"../utils/provider-guard.js\";\nimport { collectStatus } from \"../status/collect.js\";\nimport { pickSearchSlugs, loadPageRecords } from \"../search/retrieval.js\";\nimport { getPage, listPages } from \"../pages/list.js\";\nimport { listSources, getSource, deleteSource } from \"../sources/store.js\";\nimport type { CreateWikiOptions, Wiki, SdkCompileOptions } from \"./types.js\";\n\n/**\n * Run `fn` with output scoped quiet via AsyncLocalStorage.\n * Concurrent calls are fully isolated — no global flag is mutated.\n * Declared async so synchronous throws inside `fn` become rejected promises.\n */\nasync function runQuiet<T>(fn: () => Promise<T>): Promise<T> {\n  return withQuiet(fn);\n}\n\n/**\n * Create an in-process wiki facade bound to the given project root.\n *\n * @param options - `{ root }` — path to the wiki project directory.\n * @returns A `Wiki` facade whose methods delegate to the SDK-safe core.\n */\nexport function createWiki(options: CreateWikiOptions): Wiki {\n  // Normalize once so every delegated call works from an absolute path,\n  // independent of any subsequent cwd changes in the calling process.\n  const root = path.resolve(options.root);\n\n  // A missing root is valid — ingest/ingestText create sources/ via recursive mkdir.\n  // But if the path already exists and is NOT a directory, it is always a caller mistake.\n  if (existsSync(root) && !statSync(root).isDirectory()) {\n    throw new Error(`createWiki: root exists but is not a directory: ${root}`);\n  }\n\n  return {\n    ingest: ({ source }) => runQuiet(() => ingestSource(root, source)),\n\n    ingestText: (input) => runQuiet(() => ingestTextSource(root, input)),\n\n    compile: (opts: SdkCompileOptions = {}) =>\n      runQuiet(() => {\n        ensureProviderAvailable();\n        return compileAndReport(root, opts);\n      }),\n\n    search: (question) =>\n      runQuiet(async () => {\n        ensureProviderAvailable();\n        const slugs = await pickSearchSlugs(root, question);\n        return loadPageRecords(root, slugs);\n      }),\n\n    query: (question, opts = {}) =>\n      runQuiet(() => {\n        ensureProviderAvailable();\n        return generateAnswer(root, question, opts);\n      }),\n\n    getPage: (ref) => runQuiet(() => getPage(root, ref)),\n\n    listPages: (opts) => runQuiet(() => listPages(root, opts)),\n\n    listSources: (opts) => runQuiet(() => listSources(root, opts)),\n\n    getSource: (id) => runQuiet(() => getSource(root, id)),\n\n    deleteSource: (id) => runQuiet(() => deleteSource(root, id)),\n\n    status: () => runQuiet(() => collectStatus(root)),\n\n    lint: () => runQuiet(() => lint(root)),\n\n    // buildContextPack uses `prompt`/`budget` field names (NOT question/tokenBudget).\n    // Semantic retrieval is opportunistic: falls back to lexical when no embeddings\n    // are available, so no credential guard is needed here.\n    getContextPack: (opts) =>\n      runQuiet(() =>\n        buildContextPack({\n          root,\n          prompt: opts.prompt,\n          ...(opts.budget !== undefined && { budget: opts.budget }),\n          ...(opts.depth !== undefined && { depth: opts.depth }),\n          ...(opts.topPages !== undefined && { topPages: opts.topPages }),\n          ...(opts.topChunks !== undefined && { topChunks: opts.topChunks }),\n        }),\n      ),\n\n    exportJson: (opts = {}) => runQuiet(() => exportJson(root, opts)),\n\n    // \"full\" mode calls the LLM judge; \"fast\" mode is credential-free.\n    runEval: ({ mode, record = false }) =>\n      runQuiet(() => {\n        if (mode === \"full\") ensureProviderAvailable();\n        return runEval(root, mode, DEFAULT_SAMPLE_SIZE, record);\n      }),\n  };\n}\n","/**\n * ANSI colored terminal output helpers.\n * Provides consistent styling for compilation progress, status messages,\n * and streaming token display.\n *\n * Quiet-mode is scoped per async call tree via AsyncLocalStorage so that\n * concurrent SDK calls (e.g. `Promise.all([wiki.lint(), wiki.search()])`)\n * never corrupt each other's quiet state. The process-wide `quietMode` flag\n * is preserved for the `quickstart --json` code path that calls `setQuiet`\n * directly; `isQuiet()` checks the scoped value first and falls back to the\n * global flag.\n */\n\nimport { AsyncLocalStorage } from \"node:async_hooks\";\n\nconst RESET = \"\\x1b[0m\";\nconst BOLD = \"\\x1b[1m\";\nconst DIM = \"\\x1b[2m\";\nconst GREEN = \"\\x1b[32m\";\nconst YELLOW = \"\\x1b[33m\";\nconst BLUE = \"\\x1b[34m\";\nconst MAGENTA = \"\\x1b[35m\";\nconst CYAN = \"\\x1b[36m\";\nconst RED = \"\\x1b[31m\";\n\nexport function bold(text: string): string {\n  return `${BOLD}${text}${RESET}`;\n}\n\nexport function dim(text: string): string {\n  return `${DIM}${text}${RESET}`;\n}\n\nexport function success(text: string): string {\n  return `${GREEN}${text}${RESET}`;\n}\n\nexport function warn(text: string): string {\n  return `${YELLOW}${text}${RESET}`;\n}\n\nexport function info(text: string): string {\n  return `${BLUE}${text}${RESET}`;\n}\n\nexport function error(text: string): string {\n  return `${RED}${text}${RESET}`;\n}\n\nexport function source(text: string): string {\n  return `${CYAN}${text}${RESET}`;\n}\n\n/**\n * Process-wide quiet flag. Toggled by `quickstart --json` so the\n * structured envelope is the only thing on stdout — every status/header\n * call short-circuits while the flag is set.\n *\n * Default is false, preserving byte-for-byte behaviour for every other\n * command. SDK callers should use `withQuiet` instead of mutating this\n * flag directly, to avoid concurrent call corruption.\n */\nlet quietMode = false;\n\n/** ALS store scopes quietness to a single async call tree. */\nconst quietScope = new AsyncLocalStorage<boolean>();\n\n/**\n * Run `fn` with quiet mode scoped to the current async call tree.\n * Concurrent calls are fully isolated — no global flag is mutated.\n * Returns whatever `fn` returns (preserves Promise for async functions).\n */\nexport function withQuiet<T>(fn: () => T): T {\n  return quietScope.run(true, fn);\n}\n\n/**\n * Returns true if the current async context is quiet (via ALS scope)\n * or the process-wide quiet flag is set. The scoped value takes priority.\n */\nexport function isQuiet(): boolean {\n  return quietScope.getStore() ?? quietMode;\n}\n\n/** Toggle the process-wide quiet flag. */\nexport function setQuiet(quiet: boolean): void {\n  quietMode = quiet;\n}\n\n/** Print a status line with an icon. No-op while quiet mode is enabled. */\nexport function status(icon: string, message: string): void {\n  if (isQuiet()) return;\n  console.log(`${icon} ${message}`);\n}\n\n/** Print a section header. No-op while quiet mode is enabled. */\nexport function header(title: string): void {\n  if (isQuiet()) return;\n  console.log(`\\n${BOLD}${title}${RESET}`);\n  console.log(dim(\"─\".repeat(Math.min(title.length + 4, 60))));\n}\n\n/**\n * Quiet-aware warning line (stderr-style notices). No-op while quiet.\n * Writes to stderr via `console.warn` — distinct from `status()`/`header()`,\n * which write progress to stdout via `console.log`.\n */\nexport function note(message: string): void {\n  if (isQuiet()) return;\n  console.warn(message);\n}\n\n/** Read the current process-wide quiet flag. */\nexport function getQuiet(): boolean {\n  return quietMode;\n}\n","/**\n * Commander action for `llmwiki ingest <source>`.\n *\n * Detects the source type (URL, image, PDF, transcript, or generic file),\n * delegates to the appropriate ingestion module, and saves the result as a\n * markdown file with YAML frontmatter in the sources/ directory.\n *\n * Source type is persisted in frontmatter under the `sourceType` key for\n * downstream tooling and human readers.\n */\n\nimport path from \"path\";\nimport { readFile } from \"fs/promises\";\nimport { createHash } from \"node:crypto\";\nimport { buildFrontmatter } from \"../utils/markdown.js\";\nimport { saveSource } from \"../utils/source-writer.js\";\nimport { appendLog } from \"../utils/activity-log.js\";\nimport { MAX_SOURCE_CHARS, MIN_SOURCE_CHARS, SOURCES_DIR, IMAGE_EXTENSIONS, TRANSCRIPT_EXTENSIONS } from \"../utils/constants.js\";\nimport * as output from \"../utils/output.js\";\nimport ingestWeb from \"../ingest/web.js\";\nimport ingestFile from \"../ingest/file.js\";\nimport ingestPdf from \"../ingest/pdf.js\";\nimport ingestImage from \"../ingest/image.js\";\nimport ingestTranscript, { isYoutubeUrl } from \"../ingest/transcript.js\";\nimport type { IngestResult, SourceType } from \"../utils/types.js\";\n\n/** Check whether a source string looks like a URL. */\nfunction isUrl(source: string): boolean {\n  return source.startsWith(\"http://\") || source.startsWith(\"https://\");\n}\n\n/** Number of bytes to peek at when sniffing .txt content for transcript signals. */\nconst TXT_SNIFF_BYTES = 2048;\n\n/**\n * Regex for a speaker-tag line: captures the speaker name before the colon.\n * Allows names up to ~40 chars with letters, spaces, dots, apostrophes, hyphens.\n * The `gm` flags let us find ALL occurrences in the sample.\n */\nconst SPEAKER_TAG_PATTERN = /^([A-Z][a-zA-Z .'-]{0,40}):\\s/gm;\n\n/**\n * Regex for a bare timestamp at the start of a line (allowing leading\n * whitespace): \"H:MM\", \"HH:MM\", or \"HH:MM:SS\". Anchored to line starts so\n * incidental times in prose (e.g. \"the meeting at 3:00 was productive\")\n * don't trip the transcript heuristic.\n */\nconst TIMESTAMP_PATTERN = /^\\s*\\d{1,2}:\\d{2}(:\\d{2})?/;\n\n/** Minimum number of timestamp-like matches to treat a file as a transcript. */\nconst MIN_TIMESTAMP_MATCHES = 3;\n\n/**\n * Minimum number of times a single speaker name must appear to signal dialogue\n * (rules out one-off section headers like \"Summary:\" that appear only once).\n */\nconst MIN_SPEAKER_REPEAT_COUNT = 2;\n\n/**\n * Minimum number of distinct speaker names required alongside the repeat\n * condition (rules out single-speaker monologues).\n */\nconst MIN_DISTINCT_SPEAKERS = 2;\n\n/**\n * Count how many times each speaker name appears in the collected tag matches.\n * Returns a Map from name → occurrence count.\n */\nfunction countSpeakerOccurrences(sample: string): Map<string, number> {\n  const counts = new Map<string, number>();\n  // Reset lastIndex since SPEAKER_TAG_PATTERN has the `g` flag.\n  SPEAKER_TAG_PATTERN.lastIndex = 0;\n  let match: RegExpExecArray | null;\n  while ((match = SPEAKER_TAG_PATTERN.exec(sample)) !== null) {\n    const name = match[1].trim();\n    counts.set(name, (counts.get(name) ?? 0) + 1);\n  }\n  return counts;\n}\n\n/**\n * Decide whether speaker-tag occurrences in a sample look like dialogue.\n *\n * A file passes when both of the following are true:\n *  - At least {@link MIN_DISTINCT_SPEAKERS} distinct speaker names appear.\n *  - At least one name appears {@link MIN_SPEAKER_REPEAT_COUNT}+ times,\n *    indicating back-and-forth turns rather than a list of section headers\n *    (e.g. \"Summary: …\", \"Details: …\") where every label is unique.\n */\nfunction hasSpeakerDialoguePattern(sample: string): boolean {\n  const counts = countSpeakerOccurrences(sample);\n\n  const distinctSpeakers = counts.size;\n  const hasEnoughSpeakers = distinctSpeakers >= MIN_DISTINCT_SPEAKERS;\n\n  const hasRepeatedSpeaker = [...counts.values()].some(\n    (n) => n >= MIN_SPEAKER_REPEAT_COUNT,\n  );\n\n  return hasEnoughSpeakers && hasRepeatedSpeaker;\n}\n\n/**\n * Peek at the first {@link TXT_SNIFF_BYTES} of a plain-text file and decide\n * whether it looks like a conversation transcript.\n *\n * Heuristic: at least one of the following must be true in the sampled content:\n *\n *  1. **Speaker-tag dialogue pattern** — lines of the form \"Name: …\" where:\n *     - At least {@link MIN_DISTINCT_SPEAKERS} distinct names appear, AND\n *     - At least one name appears {@link MIN_SPEAKER_REPEAT_COUNT}+ times.\n *     This rejects lone section headers (\"Summary: …\") and lists of unique\n *     labels (\"Summary:\", \"Details:\", \"Notes:\") that have no repetition, while\n *     accepting real back-and-forth dialogue (\"Alice: …\\nBob: …\\nAlice: …\").\n *\n *  2. **Timestamp density** — three or more bare timestamp patterns (e.g.\n *     \"01:23\" / \"1:23:45\"), the signature of time-coded scripts or subtitles.\n *\n * When neither signal fires the caller routes the file as a generic text file.\n *\n * @param filePath - Absolute or relative path to the .txt file.\n * @returns `true` when transcript signals are detected, `false` otherwise.\n */\nasync function looksLikeTxtTranscript(filePath: string): Promise<boolean> {\n  const raw = await readFile(filePath, \"utf-8\");\n  const sample = raw.slice(0, TXT_SNIFF_BYTES);\n\n  if (hasSpeakerDialoguePattern(sample)) return true;\n\n  const timestampMatches = sample.match(new RegExp(TIMESTAMP_PATTERN.source, \"gm\"));\n  return (timestampMatches?.length ?? 0) >= MIN_TIMESTAMP_MATCHES;\n}\n\n/** Truncate result including whether truncation occurred and original length. */\ninterface TruncateResult {\n  content: string;\n  truncated: boolean;\n  originalChars: number;\n}\n\n/** Truncate content if it exceeds the character limit, logging a warning. */\nexport function enforceCharLimit(content: string): TruncateResult {\n  if (content.length <= MAX_SOURCE_CHARS) {\n    return { content, truncated: false, originalChars: content.length };\n  }\n\n  output.status(\n    \"!\",\n    output.warn(\n      `Content truncated from ${content.length.toLocaleString()} to ${MAX_SOURCE_CHARS.toLocaleString()} characters.`\n    )\n  );\n  return {\n    content: content.slice(0, MAX_SOURCE_CHARS),\n    truncated: true,\n    originalChars: content.length,\n  };\n}\n\n/** Reject empty content and warn when content is trivially short. */\nfunction enforceMinContent(content: string): void {\n  const length = content.trim().length;\n\n  if (length === 0) {\n    throw new Error(\n      \"No readable content could be extracted from the source.\"\n    );\n  }\n\n  if (length < MIN_SOURCE_CHARS) {\n    output.status(\n      \"!\",\n      output.warn(\n        `Content seems very short (${length} chars, minimum recommended is ${MIN_SOURCE_CHARS}).`\n      )\n    );\n  }\n}\n\n/**\n * Determine the source type for a given source string.\n *\n * For `.txt` files, content-sniffing is used instead of a pure extension check.\n * The file's first {@link TXT_SNIFF_BYTES} bytes are inspected for transcript\n * signals (speaker-tag lines or repeated timestamps). Only when both heuristics\n * fail is the file routed to the generic `file` adapter. `.vtt` and `.srt` are\n * always treated as transcripts regardless of content.\n *\n * @param source - A URL, local file path, or image path.\n * @returns The detected SourceType.\n */\nexport async function detectSourceType(source: string): Promise<SourceType> {\n  if (!isUrl(source)) {\n    const ext = path.extname(source).toLowerCase();\n    if (ext === \".pdf\") return \"pdf\";\n    if (IMAGE_EXTENSIONS.has(ext)) return \"image\";\n    if (TRANSCRIPT_EXTENSIONS.has(ext)) return \"transcript\";\n    if (ext === \".txt\") {\n      const isTranscript = await looksLikeTxtTranscript(source);\n      return isTranscript ? \"transcript\" : \"file\";\n    }\n    return \"file\";\n  }\n\n  if (isYoutubeUrl(source)) return \"transcript\";\n  return \"web\";\n}\n\n/** Build the full markdown document with frontmatter. */\nexport function buildDocument(\n  title: string,\n  source: string,\n  result: TruncateResult,\n  sourceType?: SourceType,\n): string {\n  const meta: Record<string, unknown> = {\n    title,\n    source,\n    ingestedAt: new Date().toISOString(),\n  };\n  if (sourceType !== undefined) {\n    meta.sourceType = sourceType;\n  }\n  if (result.truncated) {\n    meta.truncated = true;\n    meta.originalChars = result.originalChars;\n  }\n  const frontmatter = buildFrontmatter(meta);\n\n  return `${frontmatter}\\n\\n${result.content}\\n`;\n}\n\n/** Fetch content from the appropriate ingestion module based on source type. */\nasync function fetchContent(\n  source: string,\n  sourceType: SourceType,\n): Promise<{ title: string; content: string }> {\n  switch (sourceType) {\n    case \"web\":\n      return ingestWeb(source);\n    case \"pdf\":\n      return ingestPdf(source);\n    case \"image\":\n      return ingestImage(source);\n    case \"transcript\":\n      return ingestTranscript(source);\n    case \"file\":\n      return ingestFile(source);\n  }\n}\n\n/**\n * Append a root-bound ingest entry to the activity journal (`log.md`).\n * Shared by `ingestSource` and `ingestTextSource` so both ingest paths journal\n * identically: under the project `root` (not cwd) with a root-relative `Saved`\n * path, keeping the entry portable regardless of the caller's working directory.\n */\nasync function journalIngest(\n  root: string,\n  title: string,\n  source: string,\n  savedPath: string,\n  charCount: number,\n): Promise<void> {\n  await appendLog(root, \"ingest\", title, {\n    details: [\n      `Source: ${source}`,\n      `Saved: ${path.join(SOURCES_DIR, path.basename(savedPath))}`,\n      `Chars: ${charCount.toLocaleString()}`,\n    ],\n  });\n}\n\n/**\n * Programmatic ingest entry point. Identical fetch + write logic to the CLI\n * command but returns a structured IngestResult instead of writing to stdout.\n * Used by the MCP server's ingest_source tool.\n *\n * @param source - A URL (http/https), YouTube URL, local file, PDF, or image path.\n * @returns Saved filename, character count, truncation flag, source URI, and detected source type.\n */\nexport async function ingestSource(root: string, source: string): Promise<IngestResult> {\n  const sourceType = await detectSourceType(source);\n  output.status(\"*\", output.info(`Ingesting [${sourceType}]: ${source}`));\n\n  const { title, content } = await fetchContent(source, sourceType);\n\n  const result = enforceCharLimit(content);\n  enforceMinContent(result.content);\n  const document = buildDocument(title, source, result, sourceType);\n  const { path: savedPath, writeStatus } = await saveSource(root, title, document, source);\n\n  // Journal only real writes — a no-op re-ingest must not append a log line.\n  if (writeStatus !== \"unchanged\") {\n    await journalIngest(root, title, source, savedPath, result.content.length);\n  }\n\n  return {\n    filename: path.basename(savedPath),\n    charCount: result.content.length,\n    truncated: result.truncated,\n    source,\n    sourceType,\n    writeStatus,\n  };\n}\n\n/** Input shape for raw-text ingestion. */\nexport interface IngestTextInput { title: string; text: string; source?: string }\n\n/**\n * Ingest raw text directly into the wiki sources directory.\n *\n * When `source` is omitted a deterministic synthetic identity\n * `manual:<sha256(title,text)>` is derived so that identical content is\n * idempotent and differing content coexists (mirrors saveSource collision rules).\n * The hash is fed a length-prefixed title so the title/text boundary is\n * unambiguous — a raw separator (newline) or bare concatenation would let a\n * boundary-shifted pair collide (e.g. title=\"a\",text=\"b\" vs title=\"ab\",text=\"\").\n *\n * @param root - Absolute path to the wiki root directory.\n * @param input - Title, raw text body, and optional explicit source identity.\n * @returns Structured ingest result with filename, char count, and source URI.\n */\nexport async function ingestTextSource(root: string, input: IngestTextInput): Promise<IngestResult> {\n  const digest = createHash(\"sha256\")\n    .update(`${input.title.length}\\n`)\n    .update(input.title)\n    .update(input.text)\n    .digest(\"hex\");\n  const source = input.source ?? `manual:${digest}`;\n  const result = enforceCharLimit(input.text);\n  enforceMinContent(result.content);\n  const document = buildDocument(input.title, source, result, \"file\");\n  const { path: savedPath, writeStatus } = await saveSource(root, input.title, document, source);\n\n  // Journal only real writes — a no-op re-ingest must not append a log line.\n  if (writeStatus !== \"unchanged\") {\n    await journalIngest(root, input.title, source, savedPath, result.content.length);\n  }\n\n  return {\n    filename: path.basename(savedPath),\n    charCount: result.content.length,\n    truncated: result.truncated,\n    source,\n    sourceType: \"file\",\n    writeStatus,\n  };\n}\n\n/**\n * Ingest a source and save it to the sources/ directory.\n * @param source - A URL (http/https), YouTube URL, local file, PDF, or image path.\n */\nexport default async function ingest(source: string): Promise<void> {\n  const cwd = process.cwd();\n  const result = await ingestSource(cwd, source);\n  const savedPath = path.join(cwd, SOURCES_DIR, result.filename);\n\n  output.status(\n    \"+\",\n    output.success(`Saved ${output.bold(result.filename)} → ${output.source(savedPath)}`)\n  );\n  output.status(\"→\", output.dim(\"Next: llmwiki compile\"));\n}\n","/**\n * Markdown parsing and manipulation helpers.\n * Handles YAML frontmatter extraction, slugification, and atomic file writes\n * for wiki pages.\n */\n\nimport { writeFile, rename, readFile, mkdir } from \"fs/promises\";\nimport path from \"path\";\nimport yaml from \"js-yaml\";\nimport type {\n  ClaimCitation,\n  ContradictionRef,\n  ProvenanceMetadata,\n  ProvenanceState,\n  SourceSpan,\n} from \"./types.js\";\n\n/** Regex matching `^[...]` citation markers (paragraph or claim-level). */\nconst CITATION_MARKER_PATTERN = /\\^\\[([^\\]]+)\\]/g;\n\n/** Regex matching the optional `:start-end` or `#Lstart-Lend` span suffix on a citation entry. */\nconst SPAN_SUFFIX_PATTERN = /^(?<file>[^:#]+)(?:(?::(?<colonStart>\\d+)(?:[,-]\\s*(?<colonEnd>\\d+))?)|(?:#L(?<hashStart>\\d+)(?:-L(?<hashEnd>\\d+))?))?$/;\n\n/**\n * Regex matching a colon-form entry with two or more comma-separated line numbers,\n * e.g. `source.md:1, 12` or `source.md:3,7,42`. Captured `lines` is the raw\n * digit-and-comma string; each token expands into its own single-line SourceSpan.\n */\nconst COLON_MULTILINE_PATTERN = /^(?<file>[^:#]+):(?<lines>\\d+(?:,\\s*\\d+)+)$/;\n\n/** The minimum valid line number in a source span (lines are 1-indexed). */\nconst MIN_LINE_NUMBER = 1;\n\n/** The set of valid provenance state strings, used to reject unknown values. */\nconst VALID_PROVENANCE_STATES: ReadonlySet<ProvenanceState> = new Set([\n  \"extracted\",\n  \"merged\",\n  \"inferred\",\n  \"ambiguous\",\n]);\n\n/**\n * Convert a human-readable concept title to a filename slug.\n *\n * Unicode-aware: keeps letters and numbers from any script (Latin, CJK,\n * Cyrillic, Greek, Arabic, etc.). Strips punctuation, emoji, and other\n * symbols. The previous implementation used `\\w` without the `u` flag,\n * which only matches `[A-Za-z0-9_]` — that silently dropped CJK titles\n * to the empty string and caused the bug fixed in #35.\n *\n * Returns an empty string when the title contains no letters or numbers\n * at all (callers that write files should detect this and fail loudly\n * instead of writing a dotfile).\n */\nexport function slugify(title: string): string {\n  return title\n    .toLowerCase()\n    .replace(/['']/g, \"\")\n    .replace(/[^\\p{L}\\p{N}\\s-]/gu, \"\")\n    .replace(/\\s+/g, \"-\")\n    .replace(/-+/g, \"-\")\n    .replace(/^-|-$/g, \"\");\n}\n\n\nconst PROSE_LEAD_RE = /^\\p{L}/u;\n\n/**\n * Split a markdown body into prose paragraphs for eval metrics.\n * Headings, code blocks, list items, and blank lines are excluded\n * so that only human-readable claim text is counted. Used by\n * citation-coverage, citation-support, source-utilization, and\n * citation-depth so they agree on what counts as prose.\n */\nexport function splitProseParagraphs(body: string): string[] {\n  return body.split(/\\n\\s*\\n/).filter((p) => PROSE_LEAD_RE.test(p.trim()));\n}\n\n\n/** Build YAML frontmatter string from key-value pairs. */\nexport function buildFrontmatter(fields: Record<string, unknown>): string {\n  const dumped = yaml.dump(fields, { lineWidth: -1, quotingType: '\"' }).trimEnd();\n  return `---\\n${dumped}\\n---`;\n}\n\n/** Parse YAML frontmatter from a markdown string. Returns { meta, body }. */\nexport function parseFrontmatter(content: string): {\n  meta: Record<string, unknown>;\n  body: string;\n} {\n  const { meta, body } = parseFrontmatterStatus(content);\n  return { meta, body };\n}\n\n/**\n * Like `parseFrontmatter` but also reports whether a frontmatter block was\n * present and whether the YAML inside it parsed cleanly. Callers that need\n * to distinguish \"no frontmatter block\" from \"malformed YAML\" (e.g. the\n * viewer collector, which surfaces these as different warnings) use this\n * variant; the plain `parseFrontmatter` stays a thin wrapper so existing\n * callers are unaffected.\n */\nexport function parseFrontmatterStatus(content: string): {\n  meta: Record<string, unknown>;\n  body: string;\n  hasFrontmatterBlock: boolean;\n  malformedFrontmatter: boolean;\n} {\n  const match = content.match(/^---\\n([\\s\\S]*?)\\n---\\n?([\\s\\S]*)$/);\n  if (!match) {\n    return { meta: {}, body: content, hasFrontmatterBlock: false, malformedFrontmatter: false };\n  }\n\n  let meta: Record<string, unknown> = {};\n  let malformedFrontmatter = false;\n  try {\n    const parsed = yaml.load(match[1]);\n    if (parsed && typeof parsed === \"object\") {\n      meta = parsed as Record<string, unknown>;\n    } else if (parsed !== null && parsed !== undefined) {\n      // YAML parsed to a scalar/array — frontmatter must be a mapping.\n      malformedFrontmatter = true;\n    }\n  } catch {\n    malformedFrontmatter = true;\n  }\n  return { meta, body: match[2], hasFrontmatterBlock: true, malformedFrontmatter };\n}\n\n/** Atomically write a file (write to .tmp, then rename). */\nexport async function atomicWrite(filePath: string, content: string): Promise<void> {\n  await mkdir(path.dirname(filePath), { recursive: true });\n  const tmpPath = filePath + \".tmp\";\n  await writeFile(tmpPath, content, \"utf-8\");\n  await rename(tmpPath, filePath);\n}\n\n/**\n * Extract all source filenames from ^[filename.md] citation markers in a page body.\n * Handles paragraph form (`^[source.md]`), multi-source (`^[a.md, b.md]`), and the\n * claim-level extension that pins a line range (`^[source.md:42-58]` or\n * `^[source.md#L42-L58]`). Only the filename component is returned — span data is\n * discarded so existing callers continue to receive a flat filename list.\n * @param body - The markdown body text to parse.\n * @returns Array of unique source filenames.\n */\nexport function extractCitations(body: string): string[] {\n  const filenames = new Set<string>();\n  for (const citation of extractClaimCitations(body)) {\n    for (const span of citation.spans) {\n      if (span.file.length > 0) filenames.add(span.file);\n    }\n  }\n  return [...filenames];\n}\n\n/**\n * Extract claim-level citations from a markdown body. Each `^[...]` marker\n * becomes one `ClaimCitation`; comma-separated entries inside a single marker\n * become multiple spans on that citation. Entries that fail to parse against\n * the span grammar are returned as bare-file spans so callers can still tell\n * the marker was present (the linter inspects `raw` to flag malformed forms).\n * @param body - The markdown body text to parse.\n * @returns Array of ClaimCitation objects in document order.\n */\nexport function extractClaimCitations(body: string): ClaimCitation[] {\n  const citations: ClaimCitation[] = [];\n  let match: RegExpExecArray | null;\n  CITATION_MARKER_PATTERN.lastIndex = 0;\n  while ((match = CITATION_MARKER_PATTERN.exec(body)) !== null) {\n    const raw = match[1];\n    const spans = parseCitationEntries(raw);\n    if (spans.length > 0) citations.push({ raw, spans });\n  }\n  return citations;\n}\n\n/**\n * Split a raw citation marker interior (the content between `^[` and `]`) into\n * individual source-entry strings, without separating comma-separated line\n * numbers like the `12` in `source.md:1, 12`.\n *\n * The rule: split on every comma EXCEPT those followed by a purely-digit token\n * (which must be a line-number continuation). This correctly handles\n * digit-leading filenames such as `2024-notes.md`, `99problems.md`, and `1.md`.\n */\nexport function splitCitationMarker(inner: string): string[] {\n  return inner.split(/,(?!\\s*\\d+\\s*(?:,|$))/);\n}\n\n/**\n * Parse the inside of `^[...]` into one or more SourceSpan entries.\n * Delegates splitting to {@link splitCitationMarker} so `source.md:1, 12`\n * stays as one entry while digit-leading filenames like `2024-notes.md` are\n * correctly recognised as separate entries.\n */\nfunction parseCitationEntries(inner: string): SourceSpan[] {\n  const spans: SourceSpan[] = [];\n  for (const part of splitCitationMarker(inner)) {\n    const trimmed = part.trim();\n    if (trimmed.length === 0) continue;\n    spans.push(...parseSpanEntries(trimmed));\n  }\n  return spans;\n}\n\n/**\n * Dispatch a single trimmed citation entry to the right span parser.\n * Comma-separated line numbers (e.g. `file.md:1, 12`) expand into one\n * SourceSpan per line; everything else delegates to parseSpanEntry.\n */\nfunction parseSpanEntries(entry: string): SourceSpan[] {\n  const multi = COLON_MULTILINE_PATTERN.exec(entry);\n  if (multi?.groups) return parseCommaLines(multi.groups.file, multi.groups.lines);\n  const single = parseSpanEntry(entry);\n  return single !== undefined ? [single] : [];\n}\n\n/** Expand a comma-separated line-number string into individual single-line spans. */\nfunction parseCommaLines(file: string, linesStr: string): SourceSpan[] {\n  const spans: SourceSpan[] = [];\n  for (const token of linesStr.split(/,\\s*/)) {\n    const lineNum = Number(token);\n    if (isValidLineRange(lineNum, lineNum)) {\n      spans.push({ file, lines: { start: lineNum, end: lineNum } });\n    }\n  }\n  return spans;\n}\n\n/**\n * Parse a single citation entry (`file.md` / `file.md:1-3` / `file.md#L1-L3`).\n * Returns undefined when the parsed line range is semantically invalid (line\n * numbers must be >= 1 and end must be >= start).\n */\nfunction parseSpanEntry(entry: string): SourceSpan | undefined {\n  const match = SPAN_SUFFIX_PATTERN.exec(entry);\n  if (!match || !match.groups) {\n    return { file: entry };\n  }\n  const { file, colonStart, colonEnd, hashStart, hashEnd } = match.groups;\n  const start = colonStart ?? hashStart;\n  const end = colonEnd ?? hashEnd;\n  if (start === undefined) return { file };\n  const startLine = Number(start);\n  const endLine = end === undefined ? startLine : Number(end);\n  if (!isValidLineRange(startLine, endLine)) return undefined;\n  return { file, lines: { start: startLine, end: endLine } };\n}\n\n/** Returns true when both lines are >= 1 and end is not before start. */\nfunction isValidLineRange(start: number, end: number): boolean {\n  return start >= MIN_LINE_NUMBER && end >= start;\n}\n\n/**\n * Detect whether a citation entry is malformed: bracket text that contains\n * `:` or `#` characters but does not match the documented span grammar, or\n * contains a semantically invalid line range (line 0 or end before start).\n * Used by the linter to flag broken claim-level provenance markers.\n */\nexport function isMalformedCitationEntry(entry: string): boolean {\n  const trimmed = entry.trim();\n  if (trimmed.length === 0) return true;\n  if (!trimmed.includes(\":\") && !trimmed.includes(\"#\")) return false;\n  const match = SPAN_SUFFIX_PATTERN.exec(trimmed);\n  if (!match || !match.groups) return true;\n  const { colonStart, colonEnd, hashStart, hashEnd } = match.groups;\n  const start = colonStart ?? hashStart;\n  const end = colonEnd ?? hashEnd;\n  if (start === undefined) return false;\n  const startLine = Number(start);\n  const endLine = end === undefined ? startLine : Number(end);\n  return !isValidLineRange(startLine, endLine);\n}\n\n/**\n * Inspect provenance for a page body, grouping every parsed span by source file.\n * Useful for tooling that wants to render a \"this page draws from\" panel without\n * worrying about how the markers were formatted in source. Each filename maps to\n * a deduplicated list of `{start, end}` line ranges (paragraph-only citations\n * appear as the empty array, signalling \"no specific span\").\n */\nexport function inspectProvenance(body: string): Map<string, Array<{ start: number; end: number }>> {\n  const grouped = new Map<string, Array<{ start: number; end: number }>>();\n  for (const citation of extractClaimCitations(body)) {\n    for (const span of citation.spans) {\n      const ranges = grouped.get(span.file) ?? [];\n      if (span.lines && !rangeAlreadyTracked(ranges, span.lines)) {\n        ranges.push(span.lines);\n      }\n      grouped.set(span.file, ranges);\n    }\n  }\n  return grouped;\n}\n\n/** Has this start/end pair already been recorded for a file? */\nfunction rangeAlreadyTracked(\n  ranges: Array<{ start: number; end: number }>,\n  candidate: { start: number; end: number },\n): boolean {\n  return ranges.some((r) => r.start === candidate.start && r.end === candidate.end);\n}\n\n/** Read a file, returning empty string if it doesn't exist. */\nexport async function safeReadFile(filePath: string): Promise<string> {\n  try {\n    return await readFile(filePath, \"utf-8\");\n  } catch {\n    return \"\";\n  }\n}\n\n/** Parse a numeric confidence value, clamping to 0..1 and rejecting non-numbers. */\nfunction parseConfidence(raw: unknown): number | undefined {\n  if (typeof raw !== \"number\" || !Number.isFinite(raw)) return undefined;\n  if (raw < 0) return 0;\n  if (raw > 1) return 1;\n  return raw;\n}\n\n/** Parse a provenance state string, returning undefined for unknown values. */\nfunction parseProvenanceState(raw: unknown): ProvenanceState | undefined {\n  if (typeof raw !== \"string\") return undefined;\n  return VALID_PROVENANCE_STATES.has(raw as ProvenanceState)\n    ? (raw as ProvenanceState)\n    : undefined;\n}\n\n/** Coerce a single contradiction entry to a ContradictionRef, or null if invalid. */\nfunction coerceContradictionEntry(entry: unknown): ContradictionRef | null {\n  if (typeof entry === \"string\" && entry.trim().length > 0) {\n    return { slug: entry.trim() };\n  }\n  if (entry && typeof entry === \"object\" && \"slug\" in entry) {\n    const obj = entry as { slug: unknown; reason?: unknown };\n    if (typeof obj.slug !== \"string\" || obj.slug.trim().length === 0) return null;\n    const ref: ContradictionRef = { slug: obj.slug.trim() };\n    if (typeof obj.reason === \"string\") ref.reason = obj.reason;\n    return ref;\n  }\n  return null;\n}\n\n/** Parse a contradictedBy array, accepting strings or objects with slug. */\nfunction parseContradictedBy(raw: unknown): ContradictionRef[] | undefined {\n  if (!Array.isArray(raw)) return undefined;\n  const refs = raw\n    .map(coerceContradictionEntry)\n    .filter((ref): ref is ContradictionRef => ref !== null);\n  return refs.length > 0 ? refs : undefined;\n}\n\n/**\n * Extract provenance metadata fields from a parsed frontmatter record.\n * Defensively handles missing or malformed values so existing pages without\n * the new fields continue to parse correctly.\n *\n * Note: legacy pages may also carry an `inferredParagraphs` frontmatter\n * field from earlier compiles. It is intentionally not parsed here —\n * the lint rule derives the count from the rendered body instead, so\n * the cached field is ignored.\n * @param meta - Raw frontmatter object as returned by parseFrontmatter.\n * @returns Typed provenance metadata with only the fields that were present.\n */\nexport function parseProvenanceMetadata(\n  meta: Record<string, unknown>,\n): ProvenanceMetadata {\n  return {\n    confidence: parseConfidence(meta.confidence),\n    provenanceState: parseProvenanceState(meta.provenanceState),\n    contradictedBy: parseContradictedBy(meta.contradictedBy),\n  };\n}\n\n/**\n * Validate that a wiki page has non-empty content and valid frontmatter.\n * Returns true if the page is valid.\n */\nexport function validateWikiPage(content: string): boolean {\n  if (!content || content.trim().length === 0) return false;\n\n  const { meta, body } = parseFrontmatter(content);\n  if (!meta.title) return false;\n  if (body.trim().length === 0) return false;\n\n  return true;\n}\n","/**\n * Shared writer for the `sources/` directory.\n *\n * Centralises the slug → filename resolution every ingest path needs, so\n * `ingest`, `ingest-session`, and any future ingester get the same\n * protections:\n *\n *  - Empty-slug guard (#35): titles that strip to \"\" (e.g. pure emoji)\n *    fail with an actionable error instead of writing `sources/.md`.\n *  - Stable basename-collision suffix (#36): two distinct sources that\n *    slugify to the same name coexist as `name.md` and\n *    `name-<8-hex-of-source>.md`; re-ingesting the same source still\n *    overwrites in place because the existing file's frontmatter\n *    `source` field is consulted before suffixing.\n */\n\nimport { mkdir, readdir, readFile, writeFile, lstat } from \"fs/promises\";\nimport path from \"path\";\nimport { createHash } from \"crypto\";\nimport { parseFrontmatter, slugify } from \"./markdown.js\";\nimport { safeRealpath, confinedRegularFile } from \"./path-confine.js\";\nimport { SOURCES_DIR } from \"./constants.js\";\nimport { PathSafetyError } from \"../viewer/path-safety.js\";\nimport type { WriteStatus } from \"./types.js\";\n\n/** Length of the hex hash suffix appended to disambiguate basename collisions. */\nconst COLLISION_HASH_LEN = 8;\n\n/**\n * Compute a short, stable hex hash of a source identifier. Stability\n * matters — re-ingesting the same source must always produce the same\n * hash so existing files are overwritten cleanly rather than\n * accumulating duplicates.\n */\nfunction shortHashOfSource(source: string): string {\n  return createHash(\"sha256\").update(source).digest(\"hex\").slice(0, COLLISION_HASH_LEN);\n}\n\n/**\n * Resolve the destination filename for a slug + source identity when no\n * existing file owns this source (source-identity matching is handled upstream\n * by `findFileBySourceIdentity` before this is called):\n *\n * - When `${slug}.md` does not exist, return `${slug}.md`.\n * - When it exists (necessarily owned by a DIFFERENT source), return\n *   `${slug}-<hash>.md` so two distinct sources that share a basename\n *   coexist instead of one silently overwriting the other.\n */\nasync function resolveCollisionFreeFilename(\n  sourcesDir: string,\n  slug: string,\n  source: string,\n): Promise<string> {\n  const candidate = `${slug}.md`;\n  const candidatePath = path.join(sourcesDir, candidate);\n  try {\n    // No-follow existence probe: lstat never reads or follows a planted symlink\n    // at sources/<slug>.md (readFile here would EISDIR on a symlinked dir or leak\n    // an outside file). The actual write is still guarded by wx/lstat downstream.\n    await lstat(candidatePath);\n  } catch (err) {\n    if ((err as { code?: string }).code === \"ENOENT\") return candidate;\n    throw err;\n  }\n  // An entry already occupies sources/<slug>.md (a different source, or a planted\n  // symlink) — append a stable hash suffix instead of touching it.\n  return `${slug}-${shortHashOfSource(source)}.md`;\n}\n\n/**\n * Find the existing source file whose frontmatter `source` matches `source`,\n * regardless of its title-derived filename — the source identity is the key,\n * so re-ingesting under a renamed title updates the same file instead of\n * forking. O(number of sources) per ingest — reads each existing source, so\n * bulk ingest is O(n^2); a `source`->filename manifest index is the planned\n * v1.x remedy for large source sets.\n *\n * Regular files only (via `confinedRegularFile`): any symlink entry — whether\n * escaping `sourcesDir` or an in-tree alias — is skipped, keeping the scan\n * consistent with list/get/delete and preventing arbitrary-file-reads and\n * confused-deputy write-through via `saveSource`.\n */\nasync function findFileBySourceIdentity(sourcesDir: string, source: string): Promise<string | null> {\n  let names: string[];\n  try {\n    names = (await readdir(sourcesDir)).filter((f) => f.endsWith(\".md\")).sort();\n  } catch (err) {\n    if ((err as { code?: string }).code === \"ENOENT\") return null;\n    throw err;\n  }\n  for (const name of names) {\n    // Regular files only: symlinks (whether escaping or in-tree aliases) are never\n    // sources, keeping the scan consistent with list/get/delete.\n    const real = await confinedRegularFile(sourcesDir, name);\n    if (real === null) continue;\n    const { meta } = parseFrontmatter(await readFile(real, \"utf-8\"));\n    if (typeof meta.source === \"string\" && meta.source === source) return name;\n  }\n  return null;\n}\n\n/**\n * Canonical comparison key for a source document: stable frontmatter + body,\n * excluding volatile fields (`ingestedAt`). So a re-ingest with identical\n * content but a fresh timestamp is `unchanged`, while a changed title /\n * sourceType / truncation is `updated`.\n */\nfunction stableContent(document: string): string {\n  const { meta, body } = parseFrontmatter(document);\n  const stable: Record<string, unknown> = {};\n  for (const key of Object.keys(meta).sort()) {\n    if (key === \"ingestedAt\") continue;\n    stable[key] = meta[key];\n  }\n  return `${JSON.stringify(stable)}\\n${body}`;\n}\n\n/**\n * Write a markdown document into `sources/` under a slug derived from\n * the title, applying the empty-slug guard and basename-collision\n * disambiguation.\n *\n * The source identity (not the title-derived slug) is the key: if the same\n * source was previously saved under a different title, the existing file is\n * updated in place rather than forking a new file. Stable frontmatter fields\n * (title, sourceType, truncated, originalChars) are included in the\n * comparison so changed metadata is detected, but volatile fields (`ingestedAt`)\n * are excluded so a re-ingest with fresh timestamp is still `\"unchanged\"`.\n *\n * @param title - Human-readable title used to derive the filename for new sources.\n * @param document - Full markdown content (frontmatter + body) to write.\n * @param source - Source identity (URL, file path, etc.) used as the canonical\n *                 key for finding existing files and collision disambiguation.\n * @returns An object with the resolved destination `path` and a\n *          `writeStatus` of `\"created\"`, `\"updated\"`, or `\"unchanged\"`.\n */\nexport async function saveSource(\n  root: string,\n  title: string,\n  document: string,\n  source: string,\n): Promise<{ path: string; writeStatus: WriteStatus }> {\n  const slug = slugify(title);\n  // Defense in depth — even with the Unicode-aware slugifier (#35), a\n  // title made entirely of punctuation/emoji/symbols still slugifies to\n  // \"\". Without this guard the file would land at sources/.md.\n  if (!slug) {\n    throw new Error(\n      `Could not derive a filename from title \"${title}\". ` +\n        `The title contains no letter or number characters. ` +\n        `Rename the source file to one with at least one letter or digit.`,\n    );\n  }\n  // Create <root>/sources first — recursive mkdir creates a missing root + sources as\n  // real dirs (the SDK contract: a fresh, not-yet-existing root is accepted on first\n  // ingest). mkdir never follows a trailing symlink, so it won't write through a\n  // symlinked sources/.\n  await mkdir(path.join(root, SOURCES_DIR), { recursive: true });\n  // Canonicalize root and re-derive the TRUSTED sources path; reject a symlinked-away sources/.\n  const canonicalRoot = await safeRealpath(root);\n  if (canonicalRoot === null) throw new PathSafetyError(`root does not exist: ${root}`); // defensive; mkdir created it\n  const sourcesDir = path.join(canonicalRoot, SOURCES_DIR);\n  if (!(await lstat(sourcesDir)).isDirectory()) {\n    throw new PathSafetyError(`sources/ must be a real directory, not a symlink`);\n  }\n\n  // The source identity (not the title-derived slug) is the key: reuse the\n  // existing file for this source even if the title changed; only allocate a\n  // new (slug-based) filename when this is a genuinely new source.\n  const existingByIdentity = await findFileBySourceIdentity(sourcesDir, source);\n  const filename = existingByIdentity ?? (await resolveCollisionFreeFilename(sourcesDir, slug, source));\n  const destPath = path.join(sourcesDir, filename);\n\n  if (existingByIdentity === null) {\n    // New source: exclusive create — never write through a pre-existing entry\n    // (e.g. a planted symlink at the slug/hash destination).\n    try {\n      await writeFile(destPath, document, { encoding: \"utf-8\", flag: \"wx\" });\n    } catch (err) {\n      if ((err as { code?: string }).code === \"EEXIST\") {\n        throw new PathSafetyError(`refusing to write: ${filename} already exists in sources/`);\n      }\n      throw err;\n    }\n    return { path: destPath, writeStatus: \"created\" };\n  }\n  // Update: the identity scan returned an in-tree match — require a regular file\n  // (reject an intra-sources symlink target; never writeFile through a symlink).\n  if (!(await lstat(destPath)).isFile()) {\n    throw new PathSafetyError(`refusing to write: ${filename} is not a regular file`);\n  }\n  const existing = await readFile(destPath, \"utf-8\");\n  if (stableContent(existing) === stableContent(document)) {\n    return { path: destPath, writeStatus: \"unchanged\" };\n  }\n  await writeFile(destPath, document, \"utf-8\");\n  return { path: destPath, writeStatus: \"updated\" };\n}\n","/**\n * Path-confinement helpers shared by source/wiki readers. Used to drop any\n * entry whose `realpath` escapes its intended directory (e.g. a symlinked\n * `sources/leak.md` pointing outside the project), preventing local-file-read.\n *\n * Also exports `resolveSourcesDir` which additionally guards against the\n * `sources/` directory itself being a symlink to an outside location, and\n * `confinedRegularFile` — the single definition of \"a source file\" used by\n * the scan, list, get, and delete paths to stay in agreement.\n */\nimport { realpath, lstat } from \"fs/promises\";\nimport path from \"path\";\nimport { SOURCES_DIR } from \"./constants.js\";\n\n/** `realpath` that returns null instead of throwing on missing/broken paths. */\nexport async function safeRealpath(p: string): Promise<string | null> {\n  try {\n    return await realpath(p);\n  } catch {\n    return null;\n  }\n}\n\n/** True when `child` equals `dir` or sits beneath it. */\nexport function isInsideDir(child: string, dir: string): boolean {\n  if (child === dir) return true;\n  const prefix = dir.endsWith(path.sep) ? dir : dir + path.sep;\n  return child.startsWith(prefix);\n}\n\n/**\n * Resolve `dir`/`name` to its real path IF it is a confined REGULAR FILE — i.e.\n * a real file (not a symlink, not a directory) whose realpath stays within `dir`.\n * Returns null otherwise. This is the single definition of \"a source file\": a\n * symlink in `sources/` (whether escaping or an in-tree alias) is never a source,\n * keeping reads, the identity scan, and writes in agreement.\n */\nexport async function confinedRegularFile(dir: string, name: string): Promise<string | null> {\n  const entryPath = path.join(dir, name);\n  let st;\n  try {\n    st = await lstat(entryPath); // lstat: do NOT follow — a symlink must be rejected\n  } catch {\n    return null;\n  }\n  if (!st.isFile()) return null; // symlink / directory / other → not a source\n  const real = await safeRealpath(entryPath);\n  if (real === null || !isInsideDir(real, dir)) return null; // defense-in-depth\n  return real;\n}\n\n/**\n * Resolve the trusted on-disk sources directory for `root`: `<realpath(root)>/sources`,\n * requiring `sources/` to be a REAL directory at that literal path. A symlinked\n * `sources/` (which would redirect every read/write outside the project) yields null.\n * Returns null when root is missing or `sources/` is absent / not a real directory.\n */\nexport async function resolveSourcesDir(root: string): Promise<string | null> {\n  const canonicalRoot = await safeRealpath(root);\n  if (canonicalRoot === null) return null;\n  const sourcesDir = path.join(canonicalRoot, SOURCES_DIR);\n  try {\n    const st = await lstat(sourcesDir);\n    if (!st.isDirectory()) return null; // symlink or non-dir → not trusted\n  } catch {\n    return null; // missing\n  }\n  return sourcesDir;\n}\n","/**\n * Path-safety primitives for the local web viewer.\n *\n * Three layered checks form the v1 path-confinement chain. The HTTP layer\n * (Slice 2) is responsible for calling them in order at route entry:\n *\n *   1. Decode the URL path segment exactly once with `decodeURIComponent`.\n *   2. `assertSafeSlug(decoded)` — reject separators, NUL, traversal-as-slug.\n *   3. `resolveUnderRoot(root, ...segments)` — `realpath` both sides, confirm\n *      the joined target stays inside `realpath(root)`. Catches symlink\n *      escapes that survive a clean slug.\n *   4. `assertViewerSubtree(root, resolved)` — named-allowlist confinement\n *      to `wiki/`, `sources/`, and `.llmwiki/last-lint.json` only. Anything\n *      else under root (including other `.llmwiki/*`, `.git/`, `node_modules/`)\n *      is rejected even though `realpath` resolved it cleanly.\n */\n\nimport { realpath } from \"fs/promises\";\nimport path from \"path\";\nimport {\n  CONCEPTS_DIR,\n  QUERIES_DIR,\n  SOURCES_DIR,\n  LAST_LINT_FILE,\n} from \"../utils/constants.js\";\n\n/** Error thrown when any path-safety check rejects an input. */\nexport class PathSafetyError extends Error {\n  constructor(message: string) {\n    super(message);\n    this.name = \"PathSafetyError\";\n  }\n}\n\n/**\n * Reject decoded slug values that would let a request escape its intended\n * file. Run AFTER `decodeURIComponent` — percent-encoded traversal becomes\n * literal `..` here and is caught. Unicode slugs (any letter or number\n * code point) are accepted; only structural metacharacters are rejected.\n */\nexport function assertSafeSlug(decodedSlug: string): void {\n  if (typeof decodedSlug !== \"string\") {\n    throw new PathSafetyError(\"slug must be a string\");\n  }\n  if (decodedSlug.length === 0) {\n    throw new PathSafetyError(\"slug must not be empty\");\n  }\n  if (decodedSlug === \".\" || decodedSlug === \"..\") {\n    throw new PathSafetyError(`slug must not be \"${decodedSlug}\"`);\n  }\n  if (decodedSlug.includes(\"/\") || decodedSlug.includes(\"\\\\\")) {\n    throw new PathSafetyError(\"slug must not contain path separators\");\n  }\n  if (decodedSlug.includes(\"\\0\")) {\n    throw new PathSafetyError(\"slug must not contain NUL bytes\");\n  }\n  if (path.sep !== \"/\" && decodedSlug.includes(path.sep)) {\n    throw new PathSafetyError(`slug must not contain platform separator \"${path.sep}\"`);\n  }\n}\n\n/**\n * Join `root` and `safeSegments`, resolve symlinks on both ends, and\n * confirm the target stays inside `realpath(root)`. Absolute segments are\n * rejected up-front so a single bad input cannot pivot the join away from\n * `root`. Callers MUST run `assertSafeSlug` on every untrusted segment\n * before this — `resolveUnderRoot` does not re-validate slug shape.\n */\nexport async function resolveUnderRoot(\n  root: string,\n  ...safeSegments: string[]\n): Promise<string> {\n  for (const segment of safeSegments) {\n    if (typeof segment !== \"string\" || segment.length === 0) {\n      throw new PathSafetyError(\"path segment must be a non-empty string\");\n    }\n    if (path.isAbsolute(segment)) {\n      throw new PathSafetyError(\"path segment must not be absolute\");\n    }\n  }\n  const joined = path.join(root, ...safeSegments);\n  const realRoot = await realpath(root);\n  const realTarget = await realpath(joined);\n  const rootWithSep = realRoot.endsWith(path.sep) ? realRoot : realRoot + path.sep;\n  if (realTarget !== realRoot && !realTarget.startsWith(rootWithSep)) {\n    throw new PathSafetyError(\"resolved path escapes project root\");\n  }\n  return realTarget;\n}\n\n/**\n * Confine an already-resolved path to the viewer's read allowlist. The\n * spec says \"read-only metadata under `.llmwiki/`\" — encoded here as a\n * named allowlist (the single file `.llmwiki/last-lint.json`) rather than\n * the full subtree, so a future viewer addition cannot accidentally\n * expose arbitrary `.llmwiki/*` contents over HTTP.\n *\n * The function is async because both `root` and the allowlist entries\n * are canonicalized via `fs.realpath` before comparison — without that,\n * a project root that itself is a symlink (a common workflow: cloning\n * into `~/code/project` which is a symlink to `/Volumes/Work/project`)\n * would false-reject every legitimate file. Callers may pass the raw\n * project root from `process.cwd()` and trust this helper to do the\n * canonicalization. Allowlist entries that do not exist on disk fall\n * back to a non-canonicalized join, so an empty project (no `sources/`\n * yet) still has a sensible allowlist.\n */\nexport async function assertViewerSubtree(root: string, resolvedPath: string): Promise<void> {\n  const canonicalRoot = await canonicalizeOrFallback(root);\n  const allowlistDirs = await Promise.all([\n    canonicalizeOrFallback(path.join(canonicalRoot, \"wiki\")),\n    canonicalizeOrFallback(path.join(canonicalRoot, CONCEPTS_DIR)),\n    canonicalizeOrFallback(path.join(canonicalRoot, QUERIES_DIR)),\n    canonicalizeOrFallback(path.join(canonicalRoot, SOURCES_DIR)),\n  ]);\n  const lintCachePath = await canonicalizeOrFallback(path.join(canonicalRoot, LAST_LINT_FILE));\n\n  for (const dir of allowlistDirs) {\n    if (isInsideOrEqual(resolvedPath, dir)) return;\n  }\n  if (resolvedPath === lintCachePath) return;\n\n  throw new PathSafetyError(\"path is outside the viewer-approved subtrees\");\n}\n\n/**\n * Canonicalize `candidate` via `realpath`. Falls back to a normalized\n * stripped-trailing-separator string when the entry does not exist —\n * the allowlist tolerates absent directories (an empty project may have\n * no `sources/` yet) without rejecting every later check.\n */\nasync function canonicalizeOrFallback(candidate: string): Promise<string> {\n  try {\n    return await realpath(candidate);\n  } catch {\n    return candidate.endsWith(path.sep) ? candidate.slice(0, -1) : candidate;\n  }\n}\n\n/** True when `candidate` equals `parent` or sits beneath it. */\nfunction isInsideOrEqual(candidate: string, parent: string): boolean {\n  if (candidate === parent) return true;\n  const parentWithSep = parent.endsWith(path.sep) ? parent : parent + path.sep;\n  return candidate.startsWith(parentWithSep);\n}\n","/**\n * Append-only activity log (log.md).\n *\n * Implements the chronological journal described in Karpathy's llm-wiki gist:\n * a single append-only file recording what happened and when — ingests,\n * compiles, and queries. (lint is intentionally excluded: it is a read-only\n * check and the MCP `lint_wiki` tool is documented as non-mutating.) Each entry\n * is a heading line with a fixed prefix —\n * `## [YYYY-MM-DDThh:mm:ssZ] operation | description` — optionally followed by\n * a markdown bullet body carrying detail (page wikilinks, counts).\n *\n * The heading prefix is what keeps the log parseable: because only headings\n * start with `## [`, the gist's recipe `grep \"^## \\[\" log.md | tail -5` still\n * returns the five most recent operations even though entries now have bodies.\n * The log complements wiki/index.md: the index organizes content for\n * discovery, the log tracks temporal progression.\n */\n\nimport { appendFile } from \"fs/promises\";\nimport path from \"path\";\nimport {\n  LOG_FILE,\n  LOG_DESCRIPTION_MAX_CHARS,\n  LOG_MAX_PAGE_LINKS,\n} from \"./constants.js\";\nimport * as output from \"./output.js\";\n\n/** Unicode ellipsis appended when a description is truncated. */\nconst TRUNCATION_MARKER = \"…\";\n\n/** Optional extras for a log entry. */\nexport interface LogEntryOptions {\n  /** Markdown bullet detail lines rendered under the heading (page links, counts). */\n  details?: string[];\n  /** Entry timestamp; rendered as ISO 8601 UTC to second precision. Defaults to now. */\n  date?: Date;\n}\n\n/**\n * Collapse whitespace (including newlines) and cap length so the heading stays\n * a single, grep-friendly line regardless of what the caller passes in.\n */\nfunction sanitizeDescription(description: string): string {\n  const singleLine = description.replace(/\\s+/g, \" \").trim();\n  if (singleLine.length <= LOG_DESCRIPTION_MAX_CHARS) return singleLine;\n  return singleLine.slice(0, LOG_DESCRIPTION_MAX_CHARS - 1) + TRUNCATION_MARKER;\n}\n\n/**\n * Render items as a comma-separated string, truncating past `cap` with a\n * \"(+N more)\" suffix. Returns an empty string for an empty list so callers can\n * skip the detail line entirely.\n *\n * @param items - Pre-rendered list items (filenames, wikilinks, …).\n * @param cap - Max items to show before truncating; defaults to the configured limit.\n */\nexport function formatList(items: string[], cap: number = LOG_MAX_PAGE_LINKS): string {\n  const shown = items.slice(0, cap);\n  const remaining = items.length - shown.length;\n  const suffix = remaining > 0 ? `, … (+${remaining} more)` : \"\";\n  return shown.join(\", \") + suffix;\n}\n\n/**\n * Render a list of page slugs as a comma-separated wikilink string, truncating\n * past {@link LOG_MAX_PAGE_LINKS}. Returns an empty string for an empty list.\n *\n * @param slugs - Page slugs to render as `[[slug]]` wikilinks.\n * @param cap - Max links to show before truncating; defaults to the configured limit.\n */\nexport function formatWikilinkList(\n  slugs: string[],\n  cap: number = LOG_MAX_PAGE_LINKS,\n): string {\n  return formatList(slugs.map((slug) => `[[${slug}]]`), cap);\n}\n\n/**\n * Format one log entry: the parseable `## [YYYY-MM-DDThh:mm:ssZ] operation |\n * description` heading, plus a `- detail` bullet for each provided detail line.\n * Pure and date-injectable so it can be unit-tested deterministically.\n *\n * @param operation - Short operation tag, e.g. \"ingest\", \"compile\", \"query\".\n * @param description - Human-readable heading detail (title, counts, question).\n * @param date - The entry's timestamp; rendered as ISO 8601 UTC to second precision.\n * @param details - Optional bullet lines rendered under the heading.\n */\nexport function formatLogEntry(\n  operation: string,\n  description: string,\n  date: Date,\n  details: string[] = [],\n): string {\n  // ISO 8601 UTC to second precision, e.g. 2026-06-05T14:58:41Z. Sorts\n  // lexicographically and still matches the gist's `^## \\[` grep recipe.\n  const timestamp = date.toISOString().slice(0, 19) + \"Z\";\n  const heading = `## [${timestamp}] ${operation} | ${sanitizeDescription(description)}`;\n  if (details.length === 0) return heading;\n  const body = details.map((line) => `- ${line}`).join(\"\\n\");\n  return `${heading}\\n${body}`;\n}\n\n/**\n * Append a single entry to the project's log.md, blank-line separated from the\n * previous one.\n *\n * Resilient by design: the log is a side journal, so a write failure warns but\n * never throws — recording an event must not break the operation it records.\n *\n * @param root - Absolute path to the project root directory.\n * @param operation - Short operation tag, e.g. \"ingest\", \"compile\", \"query\".\n * @param description - Human-readable heading detail for the entry.\n * @param opts - Optional bullet body and entry date.\n */\nexport async function appendLog(\n  root: string,\n  operation: string,\n  description: string,\n  opts: LogEntryOptions = {},\n): Promise<void> {\n  try {\n    const entry = formatLogEntry(operation, description, opts.date ?? new Date(), opts.details);\n    await appendFile(path.join(root, LOG_FILE), `${entry}\\n\\n`, \"utf-8\");\n  } catch (err) {\n    const message = err instanceof Error ? err.message : String(err);\n    output.status(\"!\", output.warn(`Skipped log.md update: ${message}`));\n  }\n}\n","/**\n * Web URL ingestion module.\n * Fetches a URL, extracts readable content using Mozilla Readability,\n * and converts the result to clean markdown via Turndown.\n *\n * Throws descriptive errors on network failures or when the page\n * cannot be parsed into readable content.\n */\n\nimport { JSDOM } from \"jsdom\";\nimport { Readability } from \"@mozilla/readability\";\nimport TurndownService from \"turndown\";\n\ninterface WebIngestResult {\n  title: string;\n  content: string;\n}\n\n/** Fetch a URL and return its readable content as markdown. */\nasync function fetchAndParse(url: string): Promise<Response> {\n  const response = await fetch(url);\n  if (!response.ok) {\n    throw new Error(`Failed to fetch ${url}: HTTP ${response.status}`);\n  }\n  return response;\n}\n\n/** Extract readable content from raw HTML using Readability. */\nfunction extractReadableContent(html: string, url: string): { title: string; htmlContent: string } {\n  const dom = new JSDOM(html, { url });\n  const reader = new Readability(dom.window.document);\n  const article = reader.parse();\n\n  if (!article || !article.content) {\n    throw new Error(`Could not extract readable content from ${url}`);\n  }\n\n  return {\n    title: article.title || \"Untitled\",\n    htmlContent: article.content,\n  };\n}\n\n/** Convert HTML to clean markdown using Turndown. */\nfunction convertToMarkdown(html: string): string {\n  const turndown = new TurndownService({ headingStyle: \"atx\" });\n  return turndown.turndown(html);\n}\n\n/**\n * Ingest a web URL and return its content as markdown.\n * @param url - The URL to fetch and convert.\n * @returns An object with the extracted title and markdown content.\n * @throws On network failure or unparseable content.\n */\nexport default async function ingestWeb(url: string): Promise<WebIngestResult> {\n  const response = await fetchAndParse(url);\n  const html = await response.text();\n  const { title, htmlContent } = extractReadableContent(html, url);\n  const content = convertToMarkdown(htmlContent);\n\n  return { title, content };\n}\n","/**\n * Local file ingestion module.\n * Reads .md and .txt files from the local filesystem and returns their\n * content as markdown. Markdown files are returned as-is; plain text files\n * are wrapped in a markdown code block. All other extensions are rejected.\n */\n\nimport { readFile } from \"fs/promises\";\nimport path from \"path\";\nimport { titleFromFilename, type IngestedSource } from \"./shared.js\";\n\n/** Plain-text file extensions handled directly by this module. */\nconst SUPPORTED_EXTENSIONS = new Set([\".md\", \".txt\"]);\n\n/** Wrap plain text content in a markdown fenced block. */\nfunction wrapPlainText(text: string): string {\n  return `\\`\\`\\`\\n${text}\\n\\`\\`\\``;\n}\n\n/**\n * Ingest a local file and return its content as markdown.\n * @param filePath - Absolute or relative path to a .md or .txt file.\n * @returns An object with a title derived from the filename and the markdown content.\n * @throws On unsupported file type or read failure.\n */\nexport default async function ingestFile(filePath: string): Promise<IngestedSource> {\n  const ext = path.extname(filePath).toLowerCase();\n\n  if (!SUPPORTED_EXTENSIONS.has(ext)) {\n    throw new Error(\n      `Unsupported file type \"${ext}\". Only .md and .txt files are supported.`\n    );\n  }\n\n  const raw = await readFile(filePath, \"utf-8\");\n  const title = titleFromFilename(filePath);\n  const content = ext === \".md\" ? raw : wrapPlainText(raw);\n\n  return { title, content };\n}\n","/**\n * Shared helpers used by every ingest module.\n *\n * Centralizes the IngestedSource result shape and title-derivation logic so\n * each per-format ingester (file, pdf, image, transcript, web) doesn't\n * reimplement the same primitives.\n */\n\nimport path from \"path\";\n\n/** Common shape returned by every ingest module. */\nexport interface IngestedSource {\n  title: string;\n  content: string;\n}\n\n/**\n * Derive a human-readable title from a filename.\n *\n * Strips the extension and converts dashes/underscores to spaces so that\n * \"quarterly_report.pdf\" becomes \"quarterly report\".\n *\n * @param filePath - Path to a source file.\n * @returns Humanized title (lowercase preserved, no extension).\n */\nexport function titleFromFilename(filePath: string): string {\n  const basename = path.basename(filePath, path.extname(filePath));\n  return basename.replace(/[-_]+/g, \" \").trim();\n}\n","/**\n * PDF ingestion module.\n *\n * Reads a local PDF file using the pdf-parse v2 PDFParse class, extracts the\n * text content via getText() and the document metadata via getInfo(). The\n * title comes from the PDF's Info dictionary when present, falling back to\n * the filename. Pages are joined into a single markdown body.\n *\n * pdf-parse (and its transitive pdfjs-dist) is imported dynamically so the\n * cost of loading the PDF parser is only paid when a PDF is actually being\n * ingested — `node dist/cli.js --help` and every other non-PDF code path\n * stays lean.\n */\n\nimport { readFile } from \"fs/promises\";\nimport { titleFromFilename, type IngestedSource } from \"./shared.js\";\n\n/** Extract the title from PDF metadata or fall back to the filename. */\nexport function resolveTitle(filePath: string, info: unknown): string {\n  if (info && typeof info === \"object\") {\n    const titleField = (info as Record<string, unknown>)[\"Title\"];\n    if (typeof titleField === \"string\" && titleField.trim().length > 0) {\n      return titleField.trim();\n    }\n  }\n  return titleFromFilename(filePath);\n}\n\n/**\n * Ingest a local PDF file and return its text content with the document title.\n *\n * pdf-parse is imported dynamically so this module's load cost stays minimal\n * for non-PDF code paths (the parser pulls in pdfjs-dist which is sizeable).\n *\n * @param filePath - Absolute or relative path to a .pdf file.\n * @returns An object with the document title and extracted text content.\n * @throws On read failure or unparseable PDF.\n */\nexport default async function ingestPdf(filePath: string): Promise<IngestedSource> {\n  const { PDFParse } = await import(\"pdf-parse\");\n\n  const buffer = await readFile(filePath);\n  const parser = new PDFParse({ data: new Uint8Array(buffer) });\n\n  try {\n    // Sequential calls are required: pdfjs-dist's LoopbackPort.postMessage\n    // uses structuredClone internally; concurrent calls cause a DataCloneError\n    // when the port tries to transfer the same underlying state simultaneously.\n    const textResult = await parser.getText();\n    const infoResult = await parser.getInfo();\n\n    const title = resolveTitle(filePath, infoResult.info);\n    const content = textResult.text.trim();\n    return { title, content };\n  } finally {\n    await parser.destroy();\n  }\n}\n","/**\n * Image ingestion module using LLM vision capabilities.\n *\n * Reads a local image file, encodes it as base64, and sends it to the\n * configured LLM provider's vision endpoint for OCR-plus-description\n * extraction. Requires the active provider to support image content blocks\n * (currently: Anthropic).\n *\n * Throws a clear error when the provider does not support vision, rather\n * than falling back silently.\n */\n\nimport { readFile } from \"fs/promises\";\nimport path from \"path\";\nimport Anthropic from \"@anthropic-ai/sdk\";\nimport { buildAnthropicClientOptions } from \"../providers/anthropic.js\";\nimport { IMAGE_DESCRIBE_MAX_TOKENS } from \"../utils/constants.js\";\nimport { resolveAnthropicAuthFromEnv, resolveAnthropicBaseURLFromEnv, resolveAnthropicModelFromEnv } from \"../utils/claude-settings.js\";\nimport { PROVIDER_MODELS } from \"../utils/constants.js\";\nimport { titleFromFilename, type IngestedSource } from \"./shared.js\";\n\n/** Mime types supported by Anthropic vision. */\ntype AnthropicImageMediaType = \"image/jpeg\" | \"image/png\" | \"image/gif\" | \"image/webp\";\n\nconst EXTENSION_TO_MIME: Record<string, AnthropicImageMediaType> = {\n  \".jpg\": \"image/jpeg\",\n  \".jpeg\": \"image/jpeg\",\n  \".png\": \"image/png\",\n  \".gif\": \"image/gif\",\n  \".webp\": \"image/webp\",\n};\n\n/** Return the MIME type for an image file, or throw on unknown extension. */\nfunction mimeTypeForExtension(ext: string): AnthropicImageMediaType {\n  const mimeType = EXTENSION_TO_MIME[ext.toLowerCase()];\n  if (!mimeType) {\n    throw new Error(\n      `Unsupported image extension \"${ext}\". Supported: ${Object.keys(EXTENSION_TO_MIME).join(\", \")}`,\n    );\n  }\n  return mimeType;\n}\n\n/** Build an Anthropic client from the current environment config. */\nfunction buildClient(): Anthropic {\n  const baseURL = resolveAnthropicBaseURLFromEnv();\n  const auth = resolveAnthropicAuthFromEnv();\n  return new Anthropic(buildAnthropicClientOptions({ baseURL, ...auth }));\n}\n\n/** Send an image to Anthropic vision and return the extracted description. */\nasync function describeImageWithVision(\n  client: Anthropic,\n  model: string,\n  imageData: string,\n  mimeType: AnthropicImageMediaType,\n): Promise<string> {\n  const response = await client.messages.create({\n    model,\n    max_tokens: IMAGE_DESCRIBE_MAX_TOKENS,\n    messages: [\n      {\n        role: \"user\",\n        content: [\n          {\n            type: \"image\",\n            source: { type: \"base64\", media_type: mimeType, data: imageData },\n          },\n          {\n            type: \"text\",\n            text: \"Extract and transcribe all text visible in this image. Then provide a detailed description of any non-text visual content. Format your response as markdown.\",\n          },\n        ],\n      },\n    ],\n  });\n\n  const textBlock = response.content.find((block) => block.type === \"text\");\n  return textBlock?.type === \"text\" ? textBlock.text : \"\";\n}\n\n/**\n * Ingest a local image file using LLM vision for OCR and description.\n *\n * Only Anthropic is supported for vision. The active provider must be\n * Anthropic; if not, a clear error is thrown rather than degrading silently.\n *\n * @param filePath - Absolute or relative path to an image file.\n * @returns An object with a title derived from the filename and the extracted content.\n * @throws When the provider does not support vision or on read/API failure.\n */\nexport default async function ingestImage(filePath: string): Promise<IngestedSource> {\n  const providerName = process.env.LLMWIKI_PROVIDER ?? \"anthropic\";\n\n  if (providerName !== \"anthropic\") {\n    throw new Error(\n      `Image ingest requires the Anthropic provider (vision). ` +\n        `Current provider: \"${providerName}\". ` +\n        `Set LLMWIKI_PROVIDER=anthropic and ANTHROPIC_API_KEY to use image ingest.`,\n    );\n  }\n\n  const ext = path.extname(filePath).toLowerCase();\n  const mimeType = mimeTypeForExtension(ext);\n  const imageBuffer = await readFile(filePath);\n  const imageData = imageBuffer.toString(\"base64\");\n\n  const client = buildClient();\n  const model = resolveAnthropicModelFromEnv() ?? PROVIDER_MODELS.anthropic;\n  const content = await describeImageWithVision(client, model, imageData, mimeType);\n  const title = titleFromFilename(filePath);\n\n  return { title, content };\n}\n","/**\n * Anthropic LLM provider implementation.\n *\n * Wraps the @anthropic-ai/sdk to implement the LLMProvider interface.\n * Handles complete, streaming, and tool-use calls against Claude models.\n */\n\nimport Anthropic, { type ClientOptions } from \"@anthropic-ai/sdk\";\nimport type { LLMProvider, LLMMessage, LLMTool } from \"../utils/provider.js\";\nimport { voyageEmbed } from \"./voyage-embed.js\";\n\n/**\n * Builds the client options for the Anthropic SDK.\n *\n * Handles optional baseURL and filters out empty values so the SDK\n * can fall back to its internal defaults when not specified.\n */\ninterface AnthropicProviderOptions {\n  apiKey?: string;\n  authToken?: string;\n  baseURL?: string;\n}\n\nexport function buildAnthropicClientOptions(\n  options: AnthropicProviderOptions = {},\n): ClientOptions {\n  const trimmedBaseURL = options.baseURL?.trim();\n  const trimmedApiKey = options.apiKey?.trim();\n  const trimmedAuthToken = options.authToken?.trim();\n\n  const result: ClientOptions = {};\n\n  if (trimmedApiKey) {\n    result.apiKey = trimmedApiKey;\n  }\n  if (trimmedAuthToken) {\n    result.authToken = trimmedAuthToken;\n  }\n\n  if (!trimmedBaseURL) {\n    return result;\n  }\n\n  const normalizedBaseURL =\n    trimmedBaseURL.endsWith(\"/\") && trimmedBaseURL.length > 1\n      ? trimmedBaseURL.slice(0, -1)\n      : trimmedBaseURL;\n\n  result.baseURL = normalizedBaseURL;\n  return result;\n}\n\n\n/** Anthropic-backed LLM provider using the official SDK. */\nexport class AnthropicProvider implements LLMProvider {\n  private readonly client: Anthropic;\n  private readonly model: string;\n\n  constructor(model: string, options: AnthropicProviderOptions = {}) {\n    this.model = model;\n    this.client = new Anthropic(buildAnthropicClientOptions(options));\n  }\n\n  /** Send a single non-streaming completion request. */\n  async complete(system: string, messages: LLMMessage[], maxTokens: number): Promise<string> {\n    const response = await this.client.messages.create({\n      model: this.model,\n      max_tokens: maxTokens,\n      system,\n      messages,\n    });\n\n    const textBlock = response.content.find((block) => block.type === \"text\");\n    return textBlock?.type === \"text\" ? textBlock.text : \"\";\n  }\n\n  /** Stream a completion, invoking onToken for each text chunk. */\n  async stream(\n    system: string,\n    messages: LLMMessage[],\n    maxTokens: number,\n    onToken?: (text: string) => void,\n  ): Promise<string> {\n    const stream = this.client.messages.stream({\n      model: this.model,\n      max_tokens: maxTokens,\n      system,\n      messages,\n    });\n\n    let fullText = \"\";\n    for await (const event of stream) {\n      if (event.type === \"content_block_delta\" && event.delta.type === \"text_delta\") {\n        fullText += event.delta.text;\n        onToken?.(event.delta.text);\n      }\n    }\n\n    return fullText;\n  }\n\n  /** Call Claude with tool definitions and return the parsed tool input as JSON. */\n  async toolCall(\n    system: string,\n    messages: LLMMessage[],\n    tools: LLMTool[],\n    maxTokens: number,\n  ): Promise<string> {\n    const anthropicTools: Anthropic.Tool[] = tools.map((t) => ({\n      name: t.name,\n      description: t.description,\n      input_schema: t.input_schema as Anthropic.Tool.InputSchema,\n    }));\n\n    const response = await this.client.messages.create({\n      model: this.model,\n      max_tokens: maxTokens,\n      system,\n      messages,\n      tools: anthropicTools,\n      tool_choice: { type: \"any\" },\n    });\n\n    const toolBlock = response.content.find((block) => block.type === \"tool_use\");\n    if (toolBlock?.type === \"tool_use\") {\n      return JSON.stringify(toolBlock.input);\n    }\n\n    const textBlock = response.content.find((block) => block.type === \"text\");\n    return textBlock?.type === \"text\" ? textBlock.text : \"\";\n  }\n\n  /**\n   * Produce a single embedding vector via the Voyage API.\n   *\n   * Anthropic does not ship a first-party embeddings endpoint, so we delegate\n   * to Voyage (their recommended partner). Requires VOYAGE_API_KEY.\n   */\n  async embed(text: string): Promise<number[]> {\n    return voyageEmbed(text);\n  }\n}\n","/**\n * Voyage embeddings helper.\n *\n * Anthropic ships no first-party embeddings endpoint, so the Claude-backed\n * providers (`anthropic` and `claude-agent`) delegate embeddings to Voyage —\n * Anthropic's recommended partner. Shared here so both providers reuse the\n * exact same request logic. Requires the VOYAGE_API_KEY environment variable.\n */\n\nimport { EMBEDDING_MODELS } from \"../utils/constants.js\";\n\nconst VOYAGE_EMBEDDINGS_URL = \"https://api.voyageai.com/v1/embeddings\";\n\n/**\n * Produce a single embedding vector for the given text via the Voyage API.\n *\n * @param text - The text to embed.\n * @param model - Voyage model name; defaults to the Anthropic embedding model.\n * @returns The embedding vector.\n * @throws If VOYAGE_API_KEY is unset or the Voyage request fails.\n */\nexport async function voyageEmbed(\n  text: string,\n  model: string = EMBEDDING_MODELS.anthropic,\n): Promise<number[]> {\n  const apiKey = process.env.VOYAGE_API_KEY?.trim();\n  if (!apiKey) {\n    throw new Error(\n      \"VOYAGE_API_KEY is not set. Anthropic embeddings use Voyage — set VOYAGE_API_KEY to enable semantic search.\",\n    );\n  }\n\n  const response = await fetch(VOYAGE_EMBEDDINGS_URL, {\n    method: \"POST\",\n    headers: {\n      \"Content-Type\": \"application/json\",\n      Authorization: `Bearer ${apiKey}`,\n    },\n    body: JSON.stringify({ input: text, model }),\n  });\n\n  if (!response.ok) {\n    const detail = await response.text();\n    throw new Error(`Voyage embeddings request failed (${response.status}): ${detail}`);\n  }\n\n  const json = (await response.json()) as { data?: Array<{ embedding?: number[] }> };\n  const vector = json.data?.[0]?.embedding;\n  if (!Array.isArray(vector)) {\n    throw new Error(\"Voyage embeddings response did not include a vector.\");\n  }\n  return vector;\n}\n","/**\n * Transcript ingestion module.\n *\n * Handles three transcript source types:\n *   1. YouTube URLs — fetched via the youtube-transcript package.\n *   2. WebVTT (.vtt) — speaker/time markers preserved in output.\n *   3. SubRip (.srt) — speaker/time markers preserved in output.\n *   4. Plain-text (.txt) with speaker tags (e.g. \"Speaker: text\").\n *\n * Speaker and timing metadata are kept in the output so downstream\n * compilation can reference them. Content is returned as markdown.\n */\n\nimport { readFile } from \"fs/promises\";\nimport path from \"path\";\nimport { titleFromFilename, type IngestedSource } from \"./shared.js\";\n// youtube-transcript exports proper ESM via its package.json `exports` map.\n// Import from the package root; the \"import\" condition resolves to\n// ./dist/esm/index.js and includes bundled .d.ts types.\nimport { YoutubeTranscript } from \"youtube-transcript\";\n\n/** Pattern that identifies a YouTube URL. */\nconst YOUTUBE_URL_PATTERN = /^https?:\\/\\/(www\\.)?(youtube\\.com\\/watch|youtu\\.be\\/)/;\n\n/** Pattern for SRT sequence number lines (numeric-only). */\nconst SRT_SEQUENCE_PATTERN = /^\\d+$/;\n\n/** Pattern for SRT/VTT timestamp lines. */\nconst TIMESTAMP_PATTERN = /\\d{2}:\\d{2}[:.]\\d{2}/;\n\n/** Number of milliseconds in one minute. */\nconst MS_PER_MINUTE = 60_000;\n\n/** Number of milliseconds in one second. */\nconst MS_PER_SECOND = 1_000;\n\n/** Check whether a source string is a YouTube URL. */\nexport function isYoutubeUrl(source: string): boolean {\n  return YOUTUBE_URL_PATTERN.test(source);\n}\n\n/** Extract the YouTube video ID from a URL. */\nfunction extractVideoId(url: string): string {\n  const match = url.match(/(?:v=|youtu\\.be\\/)([^&?/]+)/);\n  if (!match) {\n    throw new Error(`Could not extract video ID from YouTube URL: ${url}`);\n  }\n  return match[1];\n}\n\n/** Format a millisecond offset as a \"MM:SS\" timestamp. */\nfunction formatOffset(offsetMs: number): string {\n  const minutes = Math.floor(offsetMs / MS_PER_MINUTE);\n  const seconds = Math.floor((offsetMs % MS_PER_MINUTE) / MS_PER_SECOND);\n  return `${String(minutes).padStart(2, \"0\")}:${String(seconds).padStart(2, \"0\")}`;\n}\n\n/** Fetch and format a YouTube transcript as markdown. */\nasync function fetchYoutubeTranscript(url: string): Promise<IngestedSource> {\n  const videoId = extractVideoId(url);\n  const segments = await YoutubeTranscript.fetchTranscript(videoId);\n\n  if (!segments || segments.length === 0) {\n    throw new Error(`No transcript available for YouTube video: ${url}`);\n  }\n\n  const lines = segments.map((seg) => `[${formatOffset(seg.offset)}] ${seg.text}`);\n\n  return {\n    title: `YouTube Transcript ${videoId}`,\n    content: lines.join(\"\\n\"),\n  };\n}\n\n/** Decide whether a trimmed line is a VTT/SRT cue timestamp marker. */\nfunction isCueTimestamp(trimmed: string): boolean {\n  return TIMESTAMP_PATTERN.test(trimmed) && trimmed.includes(\"-->\");\n}\n\n/** Parse a VTT file, preserving speaker cues and timestamps. */\nfunction parseVtt(raw: string, filePath: string): IngestedSource {\n  const lines = raw.split(\"\\n\");\n  const output: string[] = [];\n  let inCue = false;\n\n  for (const line of lines) {\n    const trimmed = line.trim();\n    if (trimmed === \"WEBVTT\" || trimmed === \"\") {\n      inCue = false;\n      continue;\n    }\n    if (isCueTimestamp(trimmed)) {\n      output.push(`\\n**[${trimmed}]**`);\n      inCue = true;\n      continue;\n    }\n    if (inCue && trimmed.length > 0) {\n      output.push(trimmed);\n    }\n  }\n\n  return { title: titleFromFilename(filePath), content: output.join(\"\\n\").trim() };\n}\n\n/** Parse an SRT file, preserving speaker cues and timestamps. */\nfunction parseSrt(raw: string, filePath: string): IngestedSource {\n  const lines = raw.split(\"\\n\");\n  const output: string[] = [];\n\n  for (const line of lines) {\n    const trimmed = line.trim();\n    if (trimmed === \"\" || SRT_SEQUENCE_PATTERN.test(trimmed)) {\n      continue;\n    }\n    if (isCueTimestamp(trimmed)) {\n      output.push(`\\n**[${trimmed}]**`);\n      continue;\n    }\n    if (trimmed.length > 0) {\n      output.push(trimmed);\n    }\n  }\n\n  return { title: titleFromFilename(filePath), content: output.join(\"\\n\").trim() };\n}\n\n/** Parse a plain-text transcript, preserving speaker tags. */\nfunction parsePlainTranscript(raw: string, filePath: string): IngestedSource {\n  // Plain .txt transcripts are returned as-is; speaker lines like \"Alice: ...\"\n  // are naturally readable.\n  return { title: titleFromFilename(filePath), content: raw.trim() };\n}\n\n/**\n * Ingest a transcript source: a YouTube URL or a local .vtt/.srt/.txt file.\n *\n * @param source - YouTube URL or path to a transcript file.\n * @returns Title and markdown-formatted content with speaker/time markers.\n * @throws On network failure, missing transcript, or unsupported file type.\n */\nexport default async function ingestTranscript(source: string): Promise<IngestedSource> {\n  if (isYoutubeUrl(source)) {\n    return fetchYoutubeTranscript(source);\n  }\n\n  const ext = path.extname(source).toLowerCase();\n  const raw = await readFile(source, \"utf-8\");\n\n  if (ext === \".vtt\") return parseVtt(raw, source);\n  if (ext === \".srt\") return parseSrt(raw, source);\n  if (ext === \".txt\") return parsePlainTranscript(raw, source);\n\n  throw new Error(\n    `Unsupported transcript file type \"${ext}\". Supported: .vtt, .srt, .txt`,\n  );\n}\n","/**\n * Compilation orchestrator for the llmwiki knowledge compiler.\n *\n * Coordinates the full pipeline: lock acquisition, change detection,\n * concept extraction via LLM, wiki page generation with streaming output,\n * orphan marking for deleted sources, interlink resolution, and index\n * generation. Supports incremental compilation — only new or changed\n * sources are processed through the LLM pipeline.\n */\n\nimport { readFile, readdir } from \"fs/promises\";\nimport path from \"path\";\nimport { readState, updateSourceState } from \"../utils/state.js\";\nimport {\n  buildExtractionSourceStates,\n  pickStatesForSources,\n} from \"./source-state.js\";\nimport {\n  atomicWrite,\n  buildFrontmatter,\n  parseFrontmatter,\n  safeReadFile,\n  validateWikiPage,\n  slugify,\n} from \"../utils/markdown.js\";\nimport { callClaude } from \"../utils/llm.js\";\nimport { acquireLock, releaseLock } from \"../utils/lock.js\";\nimport {\n  CONCEPT_EXTRACTION_TOOL,\n  buildExtractionPrompt,\n  buildSeedPagePrompt,\n  parseConcepts,\n} from \"./prompts.js\";\nimport { loadSchema, type SchemaConfig, type SeedPage } from \"../schema/index.js\";\nimport { detectChanges, hashFile } from \"./hasher.js\";\nimport {\n  findAffectedSources,\n  findFrozenSlugs,\n  findLateAffectedSources,\n  freezeFailedExtractions,\n  persistFrozenSlugs,\n  type ExtractionResult,\n} from \"./deps.js\";\nimport { markOrphaned, orphanUnownedFrozenPages } from \"./orphan.js\";\nimport { resolveLinks } from \"./resolver.js\";\nimport { generateIndex } from \"./indexgen.js\";\nimport { buildBudgetedCombinedContent, type SourceSlice } from \"./prompt-budget.js\";\nimport { addObsidianMeta, generateMOC } from \"./obsidian.js\";\nimport { addModelProvenanceMeta } from \"./provenance.js\";\nimport { updateEmbeddings } from \"../utils/embeddings.js\";\nimport { writeCandidate } from \"./candidates.js\";\nimport { appendLog, formatList, formatWikilinkList } from \"../utils/activity-log.js\";\nimport {\n  checkPageBrokenCitations,\n  checkPageCrossLinks,\n  checkPageMalformedCitations,\n} from \"../linter/rules.js\";\nimport type { LintResult } from \"../linter/types.js\";\nimport { renderMergedPageContent } from \"./page-renderer.js\";\nimport * as output from \"../utils/output.js\";\nimport {\n  COMPILE_CONCURRENCY,\n  CONCEPTS_DIR,\n  INDEX_FILE,\n  QUERIES_DIR,\n  SOURCES_DIR,\n} from \"../utils/constants.js\";\nimport pLimit from \"p-limit\";\nimport type {\n  CompileOptions,\n  CompileResult,\n  ExtractedConcept,\n  ReviewCandidate,\n  SourceChange,\n  SourceState,\n  WikiFrontmatter,\n  WikiState,\n} from \"../utils/types.js\";\n\n/** Per-source state snapshots keyed by source filename. */\ntype SourceStateMap = Record<string, SourceState>;\n\n/** Empty CompileResult used when no pipeline work runs (e.g. lock contention). */\nfunction emptyCompileResult(): CompileResult {\n  return { compiled: 0, skipped: 0, deleted: 0, concepts: [], pages: [], errors: [] };\n}\n\n/**\n * Run the full compilation pipeline with lock protection.\n * Acquires .llmwiki/lock, detects changes, compiles new/changed sources,\n * marks orphaned pages, resolves interlinks, and rebuilds the index.\n * @param root - Project root directory.\n * @param options - Optional pipeline overrides (e.g. --review mode).\n */\nexport async function compile(root: string, options: CompileOptions = {}): Promise<void> {\n  await compileAndReport(root, options);\n}\n\n/**\n * Run the full compilation pipeline and return a structured result.\n * Same behaviour as compile() but exposes counts, slugs, and errors so\n * non-CLI consumers (the MCP server, programmatic callers) can report\n * meaningful data without scraping terminal output.\n * @param root - Project root directory.\n * @param options - Optional pipeline overrides (e.g. --review mode).\n * @returns Structured result describing what was compiled.\n */\nexport async function compileAndReport(\n  root: string,\n  options: CompileOptions = {},\n): Promise<CompileResult> {\n  output.header(\"llmwiki compile\");\n\n  const locked = await acquireLock(root);\n  if (!locked) {\n    output.status(\"!\", output.error(\"Could not acquire lock. Try again later.\"));\n    return {\n      ...emptyCompileResult(),\n      errors: [\"Could not acquire .llmwiki/lock — another compile is in progress.\"],\n    };\n  }\n\n  try {\n    return await runCompilePipeline(root, options);\n  } finally {\n    await releaseLock(root);\n  }\n}\n\n/** Buckets of source changes used by the compile pipeline. */\ninterface ChangeBuckets {\n  toCompile: SourceChange[];\n  deleted: SourceChange[];\n  unchanged: SourceChange[];\n}\n\n/** Sort source changes into the buckets the pipeline acts on. */\nfunction bucketChanges(changes: SourceChange[]): ChangeBuckets {\n  return {\n    toCompile: changes.filter((c) => c.status === \"new\" || c.status === \"changed\"),\n    deleted: changes.filter((c) => c.status === \"deleted\"),\n    unchanged: changes.filter((c) => c.status === \"unchanged\"),\n  };\n}\n\n/** Result of phase 2: page writes plus any errors collected along the way. */\ninterface PageGenerationResult {\n  pages: MergedConcept[];\n  errors: string[];\n  /** Candidate ids written when running in --review mode. Empty otherwise. */\n  candidates: string[];\n  /**\n   * Slugs of seed pages written this run (overview / comparison / entity).\n   * Concept pages live on `pages`; seed pages don't fit MergedConcept's\n   * source-list shape, so they're tracked separately here. summarizeCompile\n   * concatenates these into CompileResult.pages so downstream consumers\n   * (MCP, embeddings, programmatic callers) see seed-page changes too.\n   */\n  seedSlugs: string[];\n}\n\n/** Phase 2: generate pages for merged concepts in parallel, capturing errors. */\nasync function generatePagesPhase(\n  root: string,\n  extractions: ExtractionResult[],\n  frozenSlugs: Set<string>,\n  schema: SchemaConfig,\n  options: CompileOptions,\n): Promise<PageGenerationResult> {\n  const merged = mergeExtractions(extractions, frozenSlugs);\n  // Build the per-source state snapshot once so each candidate can carry the\n  // exact data needed to mark its sources compiled on approval.\n  const sourceStates = options.review\n    ? await buildExtractionSourceStates(root, extractions)\n    : {};\n  const limit = pLimit(COMPILE_CONCURRENCY);\n  const errors: string[] = [];\n  const candidates: string[] = [];\n  const pages = await Promise.all(\n    merged.map((entry) => limit(async () => {\n      const result = await generateMergedPage(root, entry, schema, options, sourceStates);\n      if (result.error) errors.push(result.error);\n      if (result.candidateId) candidates.push(result.candidateId);\n      return entry;\n    })),\n  );\n  return { pages, errors, candidates, seedSlugs: [] };\n}\n\n/** Persist source state for every extraction that produced concepts. */\nasync function persistExtractionStates(\n  root: string,\n  extractions: ExtractionResult[],\n): Promise<void> {\n  for (const result of extractions) {\n    if (result.concepts.length === 0) continue;\n    await persistSourceState(root, result.sourcePath, result.sourceFile, result.concepts);\n  }\n}\n\n/**\n * Snapshot page IDs already on disk before a compile run, namespaced by\n * directory (e.g. `wiki/concepts/foo`, `wiki/queries/foo`). Namespacing keeps\n * the created/updated split correct when a concept and a query share a slug.\n */\nasync function listExistingPageIds(root: string): Promise<Set<string>> {\n  const ids = new Set<string>();\n  for (const dir of [CONCEPTS_DIR, QUERIES_DIR]) {\n    try {\n      const files = await readdir(path.join(root, dir));\n      for (const file of files) {\n        if (file.endsWith(\".md\")) ids.add(`${dir}/${file.slice(0, -3)}`);\n      }\n    } catch {\n      // Directory may not exist yet on a first compile — nothing to snapshot.\n    }\n  }\n  return ids;\n}\n\n/**\n * Journal a non-review compile to log.md: the source files consumed, plus the\n * produced pages split into created (new on disk) and updated (overwritten).\n * Compile only ever writes concept-namespace pages (concept and seed pages both\n * land under wiki/concepts/), so existence is checked against that namespace.\n */\nasync function logCompile(\n  root: string,\n  buckets: ChangeBuckets,\n  generation: PageGenerationResult,\n  existingIds: Set<string>,\n): Promise<void> {\n  if (buckets.toCompile.length === 0 && buckets.deleted.length === 0) return;\n  const produced = [...new Set([...generation.pages.map((entry) => entry.slug), ...generation.seedSlugs])];\n  const existed = (slug: string): boolean => existingIds.has(`${CONCEPTS_DIR}/${slug}`);\n  const created = produced.filter((slug) => !existed(slug));\n  const updated = produced.filter((slug) => existed(slug));\n  const heading = `${buckets.toCompile.length} source(s) → ${produced.length} page(s)`;\n  const details: string[] = [];\n  if (buckets.toCompile.length > 0) {\n    details.push(`Sources: ${formatList(buckets.toCompile.map((change) => change.file))}`);\n  }\n  if (created.length > 0) details.push(`Created: ${formatWikilinkList(created)}`);\n  if (updated.length > 0) details.push(`Updated: ${formatWikilinkList(updated)}`);\n  if (buckets.deleted.length > 0) details.push(`Deleted sources: ${buckets.deleted.length}`);\n  await appendLog(root, \"compile\", heading, { details });\n}\n\n/** Build the structured CompileResult and emit the CLI completion banner. */\nfunction summarizeCompile(\n  buckets: ChangeBuckets,\n  generation: PageGenerationResult,\n  extractions: ExtractionResult[],\n  options: CompileOptions,\n): CompileResult {\n  output.header(\"Compilation complete\");\n  output.status(\"✓\", output.success(\n    `${buckets.toCompile.length} compiled, ${buckets.unchanged.length} skipped, ${buckets.deleted.length} deleted`,\n  ));\n  if (options.review && generation.candidates.length > 0) {\n    output.status(\"?\", output.info(\n      `${generation.candidates.length} candidate(s) awaiting review — run \\`llmwiki review list\\``,\n    ));\n  } else if (buckets.toCompile.length > 0) {\n    output.status(\"→\", output.dim('Next: llmwiki query \"your question here\"'));\n  }\n\n  const errors = [...generation.errors];\n  for (const result of extractions) {\n    if (result.concepts.length === 0) {\n      errors.push(`No concepts extracted from ${result.sourceFile}`);\n    }\n  }\n\n  // Concept-page slugs first, then seed-page slugs from the same run, so\n  // downstream consumers see every page the compile actually produced.\n  // Seed pages are deterministic schema-driven writes; before this they\n  // landed on disk silently and never appeared on CompileResult.pages.\n  const conceptSlugs = generation.pages.map((entry) => entry.slug);\n  const baseResult: CompileResult = {\n    compiled: buckets.toCompile.length,\n    skipped: buckets.unchanged.length,\n    deleted: buckets.deleted.length,\n    concepts: generation.pages.map((entry) => entry.concept.concept),\n    pages: [...conceptSlugs, ...generation.seedSlugs],\n    errors,\n  };\n  if (options.review) {\n    baseResult.candidates = generation.candidates;\n  }\n  return baseResult;\n}\n\n/**\n * Apply `options.changeFilter` to the full detected change set.\n * When no filter is provided, returns the original list unchanged.\n * Separating this keeps `runCompilePipeline` below the cyclomatic threshold.\n */\nfunction applyChangeFilter(\n  detected: SourceChange[],\n  filter: CompileOptions[\"changeFilter\"],\n): SourceChange[] {\n  return filter ? detected.filter(filter) : detected;\n}\n\n/**\n * Generate seed pages unless `skipSeedPages` is set or we are in review mode.\n * Centralises both guard conditions so each call site in the pipeline is a\n * single unconditional statement instead of an inline if-block.\n */\nasync function maybeSeedPages(\n  root: string,\n  schema: SchemaConfig,\n  generation: PageGenerationResult,\n  options: CompileOptions,\n): Promise<void> {\n  if (!options.review && !options.skipSeedPages) {\n    await generateSeedPages(root, schema, generation);\n  }\n}\n\n/** Inner pipeline, runs under lock protection. Returns structured CompileResult. */\nasync function runCompilePipeline(\n  root: string,\n  options: CompileOptions,\n): Promise<CompileResult> {\n  const schema = await loadSchema(root);\n  reportSchemaStatus(schema);\n  const state = await readState(root);\n  const detected = await detectChanges(root, state);\n  const changes = applyChangeFilter(detected, options.changeFilter);\n  augmentWithAffectedSources(changes, findAffectedSources(state, changes));\n\n  const buckets = bucketChanges(changes);\n  if (buckets.toCompile.length === 0 && buckets.deleted.length === 0) {\n    output.status(\"✓\", output.success(\"Nothing to compile — all sources up to date.\"));\n    // Seed pages are cheap deterministic writes — always run them even when\n    // no source files changed, so adding a seed page to schema.json takes\n    // effect on the next compile without needing a source file edit.\n    if (!options.review) {\n      const emptyGeneration: PageGenerationResult = {\n        pages: [],\n        errors: [],\n        candidates: [],\n        seedSlugs: [],\n      };\n      await maybeSeedPages(root, schema, emptyGeneration, options);\n      // Rebuild index/MOC so the newly-written seed pages become discoverable,\n      // and propagate any seed-page validation errors into the returned result.\n      await finalizeWiki(root, emptyGeneration.pages, emptyGeneration.seedSlugs);\n      return {\n        ...emptyCompileResult(),\n        skipped: buckets.unchanged.length,\n        // Surface seed-page slugs alongside any errors so downstream\n        // consumers (MCP, embeddings, programmatic callers) can see what\n        // landed even on the no-source-changes early-return path.\n        pages: [...emptyGeneration.seedSlugs],\n        errors: emptyGeneration.errors,\n      };\n    }\n    return { ...emptyCompileResult(), skipped: buckets.unchanged.length };\n  }\n\n  printChangesSummary(changes);\n  // In review mode the pipeline contract is \"write candidates instead of\n  // mutating wiki/\". Deletion bookkeeping (orphan marking + frozen-slug\n  // persistence) writes directly into wiki/ and updates state.json, so we\n  // defer it to the next non-review compile pass. Source-state persistence\n  // for compiled sources is also review-deferred — those entries land at\n  // approve time so unapproved candidates remain re-detectable on subsequent\n  // compiles.\n  if (!options.review) {\n    await markDeletedAsOrphaned(root, buckets.deleted, state);\n  }\n\n  const frozenSlugs = findFrozenSlugs(state, changes);\n  reportFrozenSlugs(frozenSlugs);\n\n  const extractions = await runExtractionPhases(root, buckets.toCompile, state, changes);\n  if (!options.review) {\n    await freezeFailedExtractions(root, extractions, frozenSlugs);\n  }\n\n  // Snapshot pages on disk before generation so the journal can tell which\n  // produced pages are new (created) versus overwritten (updated).\n  const existingIds = await listExistingPageIds(root);\n  const generation = await generatePagesPhase(root, extractions, frozenSlugs, schema, options);\n\n  if (!options.review) {\n    await persistExtractionStates(root, extractions);\n    if (frozenSlugs.size > 0) {\n      await orphanUnownedFrozenPages(root, frozenSlugs);\n    }\n    await persistFrozenSlugs(root, frozenSlugs, extractions);\n    // Seed pages write directly into wiki/, so skip them in review mode\n    // to honour the \"no wiki/ mutation\" contract of that mode.\n    await maybeSeedPages(root, schema, generation, options);\n    await finalizeWiki(root, generation.pages, generation.seedSlugs);\n    await logCompile(root, buckets, generation, existingIds);\n  }\n  return summarizeCompile(buckets, generation, extractions, options);\n}\n\n/** Log where the schema was loaded from so the user can confirm it was picked up. */\nfunction reportSchemaStatus(schema: SchemaConfig): void {\n  if (schema.loadedFrom) {\n    output.status(\"i\", output.dim(`Schema: ${schema.loadedFrom}`));\n  }\n}\n\n/** Append affected-source changes (logging each addition) to the change list. */\nfunction augmentWithAffectedSources(changes: SourceChange[], affected: string[]): void {\n  for (const file of affected) {\n    output.status(\"~\", output.info(`${file} [affected by shared concept]`));\n    changes.push({ file, status: \"changed\" });\n  }\n}\n\n/** Mark wiki pages owned solely by deleted sources as orphaned. */\nasync function markDeletedAsOrphaned(\n  root: string,\n  deleted: SourceChange[],\n  state: WikiState,\n): Promise<void> {\n  for (const del of deleted) {\n    await markOrphaned(root, del.file, state);\n  }\n}\n\n/** Log frozen slugs (shared concepts whose deletion-pinned content must persist). */\nfunction reportFrozenSlugs(frozenSlugs: Set<string>): void {\n  for (const slug of frozenSlugs) {\n    output.status(\"i\", output.dim(`Frozen: ${slug} (shared with deleted source)`));\n  }\n}\n\n/**\n * Phase 1: extract concepts for the directly-changed batch, then expand to\n * any unchanged sources whose concepts overlap with newly extracted slugs.\n */\nasync function runExtractionPhases(\n  root: string,\n  toCompile: SourceChange[],\n  state: WikiState,\n  allChanges: SourceChange[],\n): Promise<ExtractionResult[]> {\n  const extractions: ExtractionResult[] = [];\n  for (const change of toCompile) {\n    extractions.push(await extractForSource(root, change.file));\n  }\n\n  const lateAffected = findLateAffectedSources(extractions, state, allChanges);\n  for (const file of lateAffected) {\n    output.status(\"~\", output.info(`${file} [shares concept with new source]`));\n    extractions.push(await extractForSource(root, file));\n  }\n\n  return extractions;\n}\n\n/**\n * Resolve interlinks, regenerate index/MOC, refresh embeddings\n * post-write. Seed-page slugs are folded into both the changed-slug\n * set (so embeddings refresh covers them) and the new-slug set (so\n * inbound-link resolution scans existing pages for mentions of seed\n * titles). Without that, schema-declared seed pages would land on\n * disk but stay unlinked and absent from the embedding store.\n */\nasync function finalizeWiki(\n  root: string,\n  pages: MergedConcept[],\n  seedSlugs: string[] = [],\n): Promise<void> {\n  const conceptChangedSlugs = pages.map((entry) => entry.slug);\n  const conceptNewSlugs = pages\n    .filter((entry) => entry.concept.is_new)\n    .map((entry) => entry.slug);\n  const allChangedSlugs = [...conceptChangedSlugs, ...seedSlugs];\n  const allNewSlugs = [...conceptNewSlugs, ...seedSlugs];\n\n  if (allChangedSlugs.length > 0) {\n    output.status(\"🔗\", output.info(\"Resolving interlinks...\"));\n    await resolveLinks(root, allChangedSlugs, allNewSlugs);\n  }\n\n  await generateIndex(root);\n  await generateMOC(root);\n  await safelyUpdateEmbeddings(root, allChangedSlugs);\n}\n\n/** Print a summary of detected source file changes. */\nfunction printChangesSummary(changes: SourceChange[]): void {\n  const iconMap: Record<string, string> = {\n    new: \"+\", changed: \"~\", unchanged: \".\", deleted: \"-\",\n  };\n  const fmtMap: Record<string, (s: string) => string> = {\n    new: output.success, changed: output.warn, unchanged: output.dim, deleted: output.error,\n  };\n\n  for (const c of changes) {\n    const icon = iconMap[c.status] ?? \"?\";\n    const fmt = fmtMap[c.status] ?? output.dim;\n    output.status(icon, fmt(`${c.file} [${c.status}]`));\n  }\n}\n\n/**\n * Phase 1: Extract concepts from a source without generating pages.\n * Returns extraction data for the generation phase.\n */\nasync function extractForSource(\n  root: string,\n  sourceFile: string,\n): Promise<ExtractionResult> {\n  output.status(\"*\", output.info(`Extracting: ${sourceFile}`));\n\n  const sourcePath = path.join(root, SOURCES_DIR, sourceFile);\n  const sourceContent = await readFile(sourcePath, \"utf-8\");\n  const existingIndex = await safeReadFile(path.join(root, INDEX_FILE));\n  const concepts = await extractConcepts(sourceContent, existingIndex);\n\n  if (concepts.length > 0) {\n    const names = concepts.map((c) => c.concept).join(\", \");\n    output.status(\"*\", output.dim(`  Found ${concepts.length} concepts: ${names}`));\n  }\n  return { sourceFile, sourcePath, sourceContent, concepts };\n}\n\n/** A concept with all contributing sources merged for generation. */\ninterface MergedConcept {\n  slug: string;\n  concept: ExtractedConcept;\n  sourceFiles: string[];\n  combinedContent: string;\n}\n\n/**\n * Reconcile metadata from a later-extracted concept into an existing merged entry.\n * Called when multiple sources contribute the same slug — produces the most\n * pessimistic aggregate view of confidence, provenance, and contradictions.\n *\n * Rules:\n * - confidence: min (most pessimistic value wins)\n * - provenanceState: always 'merged' once two sources are involved\n * - contradictedBy: union by slug (deduplicating on slug identity)\n *\n * `inferredParagraphs` is no longer reconciled — it is derived from the\n * rendered page body at lint time, not from extraction metadata.\n */\nexport function reconcileConceptMetadata(\n  existing: ExtractedConcept,\n  incoming: ExtractedConcept,\n): ExtractedConcept {\n  const reconciled = { ...existing };\n\n  // Minimum confidence — the weaker source's score governs the whole page.\n  if (typeof incoming.confidence === \"number\") {\n    reconciled.confidence = typeof existing.confidence === \"number\"\n      ? Math.min(existing.confidence, incoming.confidence)\n      : incoming.confidence;\n  }\n\n  // Merged state is the canonical answer when multiple sources contribute.\n  reconciled.provenanceState = \"merged\";\n\n  // Union contradictedBy entries, deduplicating by slug.\n  const refs = [...(existing.contradictedBy ?? [])];\n  const seenSlugs = new Set(refs.map((r) => r.slug));\n  for (const ref of incoming.contradictedBy ?? []) {\n    if (!seenSlugs.has(ref.slug)) {\n      refs.push(ref);\n      seenSlugs.add(ref.slug);\n    }\n  }\n  reconciled.contradictedBy = refs.length > 0 ? refs : undefined;\n\n  return reconciled;\n}\n\n/**\n * Merge extractions so each concept slug maps to ALL contributing sources.\n * When sources A and B both extract concept X, the LLM receives combined\n * content from both sources, producing a single page that reflects all\n * contributing material rather than just the last source processed.\n * Metadata is reconciled across all contributing concepts via\n * reconcileConceptMetadata so contradictions from later sources are not lost.\n *\n * Combined content is then run through {@link buildBudgetedCombinedContent}\n * so popular concepts that appear in many overlapping sources do not blow\n * past the LLM provider's context window (issue #39). When the raw total\n * fits the budget, the output is byte-identical to the previous unbudgeted\n * concatenation.\n */\nfunction mergeExtractions(\n  extractions: ExtractionResult[],\n  frozenSlugs: Set<string>,\n): MergedConcept[] {\n  const bySlug = new Map<string, MergedConcept>();\n  const slicesBySlug = new Map<string, SourceSlice[]>();\n\n  for (const result of extractions) {\n    if (result.concepts.length === 0) continue;\n\n    for (const concept of result.concepts) {\n      const slug = slugify(concept.concept);\n      if (frozenSlugs.has(slug)) continue;\n\n      const existing = bySlug.get(slug);\n      if (existing) {\n        existing.concept = reconcileConceptMetadata(existing.concept, concept);\n        existing.sourceFiles.push(result.sourceFile);\n      } else {\n        bySlug.set(slug, {\n          slug,\n          concept,\n          sourceFiles: [result.sourceFile],\n          combinedContent: \"\",\n        });\n        slicesBySlug.set(slug, []);\n      }\n      slicesBySlug.get(slug)!.push({\n        file: result.sourceFile,\n        content: result.sourceContent,\n      });\n    }\n  }\n\n  for (const merged of bySlug.values()) {\n    const slices = slicesBySlug.get(merged.slug) ?? [];\n    merged.combinedContent = buildBudgetedCombinedContent(\n      merged.concept.concept,\n      slices,\n    );\n  }\n\n  return Array.from(bySlug.values());\n}\n\n/** Outcome of generating a single merged concept page. */\ninterface MergedPageOutcome {\n  error?: string;\n  candidateId?: string;\n}\n\n/**\n * Generate a wiki page from merged source content.\n * For shared concepts, the LLM sees content from all contributing sources\n * and frontmatter records every source file. When `options.review` is set,\n * the rendered page is persisted as a review candidate instead of being\n * written into `wiki/`.\n */\nasync function generateMergedPage(\n  root: string,\n  entry: MergedConcept,\n  schema: SchemaConfig,\n  options: CompileOptions,\n  sourceStates: SourceStateMap,\n): Promise<MergedPageOutcome> {\n  const fullPage = await renderMergedPageContent(root, entry, schema);\n\n  if (options.review) {\n    return await persistReviewCandidate(root, entry, fullPage, sourceStates, schema);\n  }\n\n  const pagePath = path.join(root, CONCEPTS_DIR, `${entry.slug}.md`);\n  const error = await writePageIfValid(pagePath, fullPage, entry.concept.concept);\n  return { error: error ?? undefined };\n}\n\n/** Persist a candidate JSON record for later review and report it on stdout. */\nasync function persistReviewCandidate(\n  root: string,\n  entry: MergedConcept,\n  fullPage: string,\n  sourceStates: SourceStateMap,\n  schema: SchemaConfig,\n): Promise<MergedPageOutcome> {\n  // Run schema-aware AND provenance-aware lint against the candidate body so\n  // both classes of violation are visible in `review show` before a reviewer\n  // approves the page. The virtual file path uses the slug so diagnostics\n  // are identifiable without a real disk path. Provenance lint covers the\n  // citation rules that previously only ran on the post-promotion compile.\n  const virtualPath = `wiki/concepts/${entry.slug}.md`;\n  const schemaViolations = checkPageCrossLinks(fullPage, virtualPath, schema);\n  const provenanceViolations = await collectCandidateProvenanceViolations(\n    root,\n    fullPage,\n    virtualPath,\n  );\n\n  const candidate: ReviewCandidate = await writeCandidate(root, {\n    title: entry.concept.concept,\n    slug: entry.slug,\n    summary: entry.concept.summary,\n    sources: entry.sourceFiles,\n    body: fullPage,\n    sourceStates: pickStatesForSources(sourceStates, entry.sourceFiles),\n    schemaViolations: schemaViolations.length > 0 ? schemaViolations : undefined,\n    provenanceViolations:\n      provenanceViolations.length > 0 ? provenanceViolations : undefined,\n  });\n  output.status(\"?\", output.info(`Candidate ready: ${candidate.id} (${entry.slug})`));\n  return { candidateId: candidate.id };\n}\n\n/**\n * Run the in-memory provenance lint rules against a candidate body:\n * malformed claim citations + broken-source / out-of-bounds line spans.\n * Returns the combined diagnostics so writeCandidate can persist them.\n */\nasync function collectCandidateProvenanceViolations(\n  root: string,\n  fullPage: string,\n  virtualPath: string,\n): Promise<LintResult[]> {\n  const malformed = checkPageMalformedCitations(fullPage, virtualPath);\n  const broken = await checkPageBrokenCitations(\n    fullPage,\n    virtualPath,\n    path.join(root, SOURCES_DIR),\n  );\n  return [...malformed, ...broken];\n}\n\n/**\n * Materialise schema-declared seed pages (overview, comparison, entity).\n * Each seed page is written under wiki/concepts/ next to concept pages so\n * existing tooling (index, MOC, lint, embeddings) treats them uniformly.\n * Slugs from generated pages this run are added so seed pages can be linked\n * deterministically without waiting for a second compile pass.\n * @param root - Project root directory.\n * @param schema - Resolved schema config.\n * @param generation - Result of the concept-page generation phase.\n */\nasync function generateSeedPages(\n  root: string,\n  schema: SchemaConfig,\n  generation: PageGenerationResult,\n): Promise<void> {\n  if (schema.seedPages.length === 0) return;\n  for (const seed of schema.seedPages) {\n    const result = await generateSingleSeedPage(root, schema, seed);\n    if (result.error) {\n      generation.errors.push(result.error);\n      continue;\n    }\n    generation.seedSlugs.push(result.slug);\n  }\n}\n\n/** Outcome of a single seed-page generation: slug always, error when the write failed validation. */\ninterface SeedPageOutcome {\n  slug: string;\n  error?: string;\n}\n\n/** Build, prompt, and persist a single seed page. */\nasync function generateSingleSeedPage(\n  root: string,\n  schema: SchemaConfig,\n  seed: SeedPage,\n): Promise<SeedPageOutcome> {\n  const slug = slugify(seed.title);\n  const pagePath = path.join(root, CONCEPTS_DIR, `${slug}.md`);\n  const relatedContent = await loadSeedRelatedPages(root, seed.relatedSlugs ?? []);\n  const rule = schema.kinds[seed.kind];\n  const system = buildSeedPagePrompt(seed, rule, relatedContent);\n  const pageBody = await callClaude({\n    system,\n    messages: [{ role: \"user\", content: `Write the ${seed.kind} page titled \"${seed.title}\".` }],\n  });\n\n  const now = new Date().toISOString();\n  const existing = await safeReadFile(pagePath);\n  const existingMeta = existing ? parseFrontmatter(existing).meta : null;\n  const createdAt = typeof existingMeta?.createdAt === \"string\" ? existingMeta.createdAt : now;\n  const typedFields: WikiFrontmatter = {\n    title: seed.title,\n    summary: seed.summary,\n    sources: [],\n    kind: seed.kind,\n    createdAt,\n    updatedAt: now,\n  };\n  const frontmatterFields: Record<string, unknown> = { ...typedFields };\n  addObsidianMeta(frontmatterFields, seed.title, []);\n  addModelProvenanceMeta(frontmatterFields);\n  const frontmatter = buildFrontmatter(frontmatterFields);\n  const error = await writePageIfValid(pagePath, `${frontmatter}\\n\\n${pageBody}\\n`, seed.title);\n  return error ? { slug, error } : { slug };\n}\n\n/** Load the bodies of the related concept pages a seed page should weave together. */\nasync function loadSeedRelatedPages(root: string, slugs: string[]): Promise<string> {\n  if (slugs.length === 0) return \"\";\n  const contents: string[] = [];\n  for (const slug of slugs) {\n    const pagePath = path.join(root, CONCEPTS_DIR, `${slug}.md`);\n    const content = await safeReadFile(pagePath);\n    if (content) contents.push(content);\n  }\n  return contents.join(\"\\n\\n---\\n\\n\");\n}\n\n/**\n * Call Claude to extract concepts from a source document.\n * @param sourceContent - Full source document text.\n * @param existingIndex - Current wiki index for deduplication.\n * @returns Parsed array of extracted concepts.\n */\nasync function extractConcepts(\n  sourceContent: string,\n  existingIndex: string,\n): Promise<ExtractedConcept[]> {\n  const system = buildExtractionPrompt(sourceContent, existingIndex);\n  const rawOutput = await callClaude({\n    system,\n    messages: [{ role: \"user\", content: \"Extract the key concepts from this source.\" }],\n    tools: [CONCEPT_EXTRACTION_TOOL],\n  });\n\n  return parseConcepts(rawOutput);\n}\n\n/**\n * Validate and atomically write a wiki page, logging the result.\n * @param pagePath - Absolute path to write the page.\n * @param content - Full page content including frontmatter.\n * @param conceptTitle - Title for logging purposes.\n */\nasync function writePageIfValid(\n  pagePath: string,\n  content: string,\n  conceptTitle: string,\n): Promise<string | null> {\n  if (!validateWikiPage(content)) {\n    output.status(\"!\", output.warn(`Invalid page for \"${conceptTitle}\" — skipped.`));\n    return `Invalid page for \"${conceptTitle}\" — failed validation`;\n  }\n\n  await atomicWrite(pagePath, content);\n  return null;\n}\n\n/**\n * Refresh the embeddings store without failing compilation.\n * Semantic search is a non-critical enhancement — missing API keys or\n * transient provider errors should produce a warning, not a broken build.\n */\nasync function safelyUpdateEmbeddings(root: string, changedSlugs: string[]): Promise<void> {\n  try {\n    await updateEmbeddings(root, changedSlugs);\n  } catch (err) {\n    const message = err instanceof Error ? err.message : String(err);\n    output.status(\"!\", output.warn(`Skipped embeddings update: ${message}`));\n  }\n}\n\n/**\n * Update the persisted state for a compiled source file.\n * @param root - Project root directory.\n * @param sourcePath - Absolute path to the source file.\n * @param sourceFile - Filename within sources/.\n * @param concepts - Concepts extracted from this source.\n */\nasync function persistSourceState(\n  root: string,\n  sourcePath: string,\n  sourceFile: string,\n  concepts: ReturnType<typeof parseConcepts>,\n): Promise<void> {\n  const hash = await hashFile(sourcePath);\n  const entry: SourceState = {\n    hash,\n    concepts: concepts.map((c) => slugify(c.concept)),\n    compiledAt: new Date().toISOString(),\n  };\n\n  await updateSourceState(root, sourceFile, entry);\n}\n","/**\n * Manages .llmwiki/state.json — the persistent compilation state that tracks\n * source file hashes and their compiled concepts. Enables incremental\n * compilation by detecting which sources have changed since last compile.\n *\n * Uses atomic writes (write to .tmp, then rename) to prevent corruption\n * from interrupted compiles.\n */\n\nimport { readFile, writeFile, rename, mkdir, copyFile } from \"fs/promises\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport { LLMWIKI_DIR, STATE_FILE } from \"./constants.js\";\nimport { note } from \"./output.js\";\nimport type { WikiState, SourceState } from \"./types.js\";\n\nfunction emptyState(): WikiState {\n  return { version: 1, indexHash: \"\", sources: {} };\n}\n\n/** State file read outcome: ok = parsed, missing = no file, corrupt = unparseable. */\nexport interface ClassifiedState {\n  status: \"ok\" | \"missing\" | \"corrupt\";\n  state: WikiState;\n}\n\n/**\n * Read .llmwiki/state.json and classify the outcome WITHOUT side effects.\n * Unlike readState(), this never writes a .bak on corrupt input, so read-only\n * callers (freshness/lint/view/export) can safely use it.\n */\nexport async function readStateClassified(root: string): Promise<ClassifiedState> {\n  const filePath = path.join(root, STATE_FILE);\n  if (!existsSync(filePath)) return { status: \"missing\", state: emptyState() };\n  try {\n    const raw = await readFile(filePath, \"utf-8\");\n    return { status: \"ok\", state: JSON.parse(raw) as WikiState };\n  } catch {\n    return { status: \"corrupt\", state: emptyState() };\n  }\n}\n\n/** Read .llmwiki/state.json, recovering from corruption gracefully (writes a .bak). */\nexport async function readState(root: string): Promise<WikiState> {\n  const classified = await readStateClassified(root);\n  if (classified.status === \"corrupt\") {\n    const filePath = path.join(root, STATE_FILE);\n    const bakPath = filePath + \".bak\";\n    note(`⚠ Corrupt state.json — backed up to ${bakPath}, starting fresh.`);\n    await copyFile(filePath, bakPath);\n  }\n  return classified.state;\n}\n\n/** Atomically write state.json (write .tmp then rename). */\nexport async function writeState(root: string, state: WikiState): Promise<void> {\n  const dir = path.join(root, LLMWIKI_DIR);\n  await mkdir(dir, { recursive: true });\n\n  const filePath = path.join(root, STATE_FILE);\n  const tmpPath = filePath + \".tmp\";\n\n  await writeFile(tmpPath, JSON.stringify(state, null, 2), \"utf-8\");\n  await rename(tmpPath, filePath);\n}\n\n/**\n * Update a single source's entry in state after successful compilation.\n * Per-source granularity means interrupted compiles only reprocess incomplete sources.\n */\nexport async function updateSourceState(\n  root: string,\n  sourceFile: string,\n  entry: SourceState,\n): Promise<void> {\n  const state = await readState(root);\n  state.sources[sourceFile] = entry;\n  await writeState(root, state);\n}\n\n/** Remove a source entry from state (for deleted sources). */\nexport async function removeSourceState(\n  root: string,\n  sourceFile: string,\n): Promise<void> {\n  const state = await readState(root);\n  delete state.sources[sourceFile];\n  await writeState(root, state);\n}\n","/**\n * Source-state snapshot helpers shared between the live compile path and the\n * review-candidate path.\n *\n * The compile pipeline normally persists a `SourceState` entry for every\n * extracted source so subsequent compiles can skip unchanged inputs. When\n * compile runs in `--review` mode, page writes are deferred — but the same\n * per-source state still needs to land on approval, otherwise approved\n * sources stay marked as \"new/changed\" forever and reproduce duplicate\n * candidates on every compile.\n *\n * This module produces a `Record<sourceFile, SourceState>` snapshot from the\n * extraction results so it can ride along inside each `ReviewCandidate` and\n * be flushed to `.llmwiki/state.json` at approval time.\n */\n\nimport path from \"path\";\nimport { hashFile } from \"./hasher.js\";\nimport { slugify } from \"../utils/markdown.js\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\nimport type { ExtractionResult } from \"./deps.js\";\nimport type { SourceState } from \"../utils/types.js\";\n\n/**\n * Compute a per-source state snapshot keyed by source filename.\n *\n * Hashes every contributing source once so each candidate carries the\n * incremental-state payload required to mark its sources compiled on\n * approval. Sources with no extracted concepts are skipped — we only mark\n * sources compiled when extraction succeeded, mirroring the live path's\n * behaviour.\n *\n * @param root - Project root directory.\n * @param extractions - Extraction results from the compile pipeline.\n * @returns Map of source filename → SourceState ready for state.json.\n */\nexport async function buildExtractionSourceStates(\n  root: string,\n  extractions: ExtractionResult[],\n): Promise<Record<string, SourceState>> {\n  const snapshot: Record<string, SourceState> = {};\n  const compiledAt = new Date().toISOString();\n\n  for (const result of extractions) {\n    if (result.concepts.length === 0) continue;\n    snapshot[result.sourceFile] = await buildEntry(root, result, compiledAt);\n  }\n\n  return snapshot;\n}\n\n/** Build a single SourceState entry for one extraction result. */\nasync function buildEntry(\n  root: string,\n  result: ExtractionResult,\n  compiledAt: string,\n): Promise<SourceState> {\n  const filePath = path.join(root, SOURCES_DIR, result.sourceFile);\n  const hash = await hashFile(filePath);\n  return {\n    hash,\n    concepts: result.concepts.map((concept) => slugify(concept.concept)),\n    compiledAt,\n  };\n}\n\n/**\n * Filter a global source-state snapshot down to entries relevant to a\n * specific candidate. A candidate carries only the source-state entries\n * for sources that actually contributed to it, so on approval we can\n * persist a minimal, accurate slice into state.json.\n *\n * @param allStates - Global per-source snapshot from buildExtractionSourceStates.\n * @param sourceFiles - Source filenames that contributed to the candidate.\n */\nexport function pickStatesForSources(\n  allStates: Record<string, SourceState>,\n  sourceFiles: string[],\n): Record<string, SourceState> {\n  const picked: Record<string, SourceState> = {};\n  for (const file of sourceFiles) {\n    const entry = allStates[file];\n    if (entry) picked[file] = entry;\n  }\n  return picked;\n}\n","/**\n * Source file hashing for change detection.\n * Computes SHA-256 hashes of source files and compares them against\n * previously stored state to determine which files need recompilation.\n * This enables incremental compilation — only changed or new sources\n * are sent through the LLM pipeline.\n */\n\nimport { createHash } from \"node:crypto\";\nimport { readFile, readdir } from \"fs/promises\";\nimport path from \"path\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\nimport type { WikiState, SourceChange } from \"../utils/types.js\";\n\n/**\n * Read a file and compute its SHA-256 hash.\n * @param filePath - Absolute path to the file to hash.\n * @returns Hex-encoded SHA-256 digest of the file contents.\n */\nexport async function hashFile(filePath: string): Promise<string> {\n  const content = await readFile(filePath, \"utf-8\");\n  return createHash(\"sha256\").update(content).digest(\"hex\");\n}\n\n/**\n * Scan the sources/ directory and compare file hashes against previous state\n * to identify new, changed, unchanged, and deleted source files.\n * @param root - Project root directory containing the sources/ folder.\n * @param prevState - The previously persisted WikiState to compare against.\n * @returns Array of SourceChange entries describing each file's status.\n */\nexport async function detectChanges(\n  root: string,\n  prevState: WikiState,\n): Promise<SourceChange[]> {\n  const sourcesPath = path.join(root, SOURCES_DIR);\n  const currentFiles = await listSourceFiles(sourcesPath);\n  const changes: SourceChange[] = [];\n\n  for (const file of currentFiles) {\n    const status = await classifyFile(root, file, prevState);\n    changes.push({ file, status });\n  }\n\n  const deletedChanges = findDeletedFiles(currentFiles, prevState);\n  changes.push(...deletedChanges);\n\n  return changes;\n}\n\n/**\n * List all markdown files in the sources directory.\n * @param sourcesPath - Absolute path to the sources/ directory.\n * @returns Array of filenames (not full paths).\n */\nasync function listSourceFiles(sourcesPath: string): Promise<string[]> {\n  try {\n    const entries = await readdir(sourcesPath);\n    return entries.filter((f) => f.endsWith(\".md\"));\n  } catch {\n    return [];\n  }\n}\n\n/**\n * Classify a single source file as new, changed, or unchanged.\n * @param root - Project root directory.\n * @param file - Filename within sources/.\n * @param prevState - Previous compilation state.\n * @returns The change status for this file.\n */\nasync function classifyFile(\n  root: string,\n  file: string,\n  prevState: WikiState,\n): Promise<SourceChange[\"status\"]> {\n  const filePath = path.join(root, SOURCES_DIR, file);\n  const hash = await hashFile(filePath);\n  const prev = prevState.sources[file];\n\n  if (!prev) return \"new\";\n  if (prev.hash !== hash) return \"changed\";\n  return \"unchanged\";\n}\n\n/**\n * Find source files present in previous state but missing from disk.\n * @param currentFiles - Files currently on disk.\n * @param prevState - Previous compilation state.\n * @returns Array of SourceChange entries for deleted files.\n */\nfunction findDeletedFiles(\n  currentFiles: string[],\n  prevState: WikiState,\n): SourceChange[] {\n  const currentSet = new Set(currentFiles);\n  return Object.keys(prevState.sources)\n    .filter((file) => !currentSet.has(file))\n    .map((file) => ({ file, status: \"deleted\" as const }));\n}\n","/**\n * OpenAI LLM provider implementation.\n *\n * Wraps the openai npm package to implement the LLMProvider interface.\n * Translates Anthropic-style tool schemas (input_schema) to OpenAI format (parameters).\n */\n\nimport OpenAI from \"openai\";\nimport type { LLMProvider, LLMMessage, LLMTool } from \"../utils/provider.js\";\nimport { EMBEDDING_MODELS, OPENAI_DEFAULT_TIMEOUT_MS } from \"../utils/constants.js\";\n\n/** Construction options for an OpenAI-compatible provider. */\ninterface OpenAIProviderOptions {\n  baseURL?: string;\n  apiKey?: string;\n  embeddingsBaseURL?: string;\n  embeddingModel?: string;\n  /**\n   * Per-request timeout in milliseconds. Defaults to 10 minutes for cloud\n   * OpenAI (matches the SDK default). Long compile-time completions on\n   * slower local models can exceed this — see {@link OllamaProvider} which\n   * raises the default and reads LLMWIKI_REQUEST_TIMEOUT_MS / OLLAMA_TIMEOUT_MS.\n   */\n  timeoutMs?: number;\n}\n\n/**\n * Read an integer-millisecond timeout from an env var. Returns undefined when\n * the env var is unset, empty, non-numeric, zero, or negative — so the caller\n * silently falls back to the next source in its resolution chain (env-var\n * typos like `OLLAMA_TIMEOUT_MS=30m` are not surfaced to the user).\n */\nexport function readTimeoutEnv(name: string): number | undefined {\n  const raw = process.env[name]?.trim();\n  if (!raw) return undefined;\n  const parsed = Number(raw);\n  return Number.isFinite(parsed) && parsed > 0 ? parsed : undefined;\n}\n\n/** Resolve the OpenAI client timeout from LLMWIKI_REQUEST_TIMEOUT_MS, if set. */\nfunction resolveOpenAITimeoutMs(): number | undefined {\n  return readTimeoutEnv(\"LLMWIKI_REQUEST_TIMEOUT_MS\");\n}\n\n/**\n * Placeholder passed to the OpenAI client when no real key is set. The SDK (v6+)\n * throws on a missing/empty key at construction, but real credential validation\n * is owned by `ensureProviderAvailable` (the provider guard); deferring here\n * keeps that the single source of truth. Local servers that ignore auth accept\n * any value anyway.\n */\nconst PLACEHOLDER_API_KEY = \"llmwiki-unset\";\n\n/** Translate an Anthropic-style LLMTool to an OpenAI ChatCompletionTool. */\nexport function translateToolToOpenAI(\n  tool: LLMTool,\n): OpenAI.ChatCompletionTool {\n  return {\n    type: \"function\",\n    function: {\n      name: tool.name,\n      description: tool.description,\n      parameters: tool.input_schema,\n    },\n  };\n}\n\n/** OpenAI-backed LLM provider. */\nexport class OpenAIProvider implements LLMProvider {\n  protected readonly client: OpenAI;\n  protected readonly embeddingsClient: OpenAI;\n  protected readonly model: string;\n  protected readonly configuredEmbeddingModel?: string;\n\n  constructor(model: string, options: OpenAIProviderOptions = {}) {\n    this.model = model;\n    this.configuredEmbeddingModel = options.embeddingModel;\n    // The OpenAI SDK (v6+) throws on a missing/empty key at construction. Real\n    // credential validation is owned by the provider guard, so pass a\n    // placeholder when unset to defer the check to that single source of truth.\n    const resolvedKey = options.apiKey ?? process.env.OPENAI_API_KEY ?? PLACEHOLDER_API_KEY;\n    const timeout = options.timeoutMs ?? resolveOpenAITimeoutMs() ?? OPENAI_DEFAULT_TIMEOUT_MS;\n    this.client = new OpenAI({\n      apiKey: resolvedKey,\n      baseURL: options.baseURL ?? null,\n      timeout,\n    });\n    this.embeddingsClient = options.embeddingsBaseURL\n      ? new OpenAI({ apiKey: resolvedKey, baseURL: options.embeddingsBaseURL, timeout })\n      : this.client;\n  }\n\n  /** Send a single non-streaming completion request. */\n  async complete(system: string, messages: LLMMessage[], maxTokens: number): Promise<string> {\n    const response = await this.client.chat.completions.create({\n      model: this.model,\n      max_tokens: maxTokens,\n      messages: [{ role: \"system\", content: system }, ...messages],\n    });\n\n    return response.choices[0]?.message?.content ?? \"\";\n  }\n\n  /** Stream a completion, invoking onToken for each text chunk. */\n  async stream(\n    system: string,\n    messages: LLMMessage[],\n    maxTokens: number,\n    onToken?: (text: string) => void,\n  ): Promise<string> {\n    const stream = await this.client.chat.completions.create({\n      model: this.model,\n      max_tokens: maxTokens,\n      messages: [{ role: \"system\", content: system }, ...messages],\n      stream: true,\n    });\n\n    let fullText = \"\";\n    for await (const chunk of stream) {\n      const delta = chunk.choices[0]?.delta?.content;\n      if (delta) {\n        fullText += delta;\n        onToken?.(delta);\n      }\n    }\n\n    return fullText;\n  }\n\n  /** Call the model with tool definitions and return the parsed tool input as JSON. */\n  async toolCall(\n    system: string,\n    messages: LLMMessage[],\n    tools: LLMTool[],\n    maxTokens: number,\n  ): Promise<string> {\n    const openaiTools = tools.map(translateToolToOpenAI);\n\n    const response = await this.client.chat.completions.create({\n      model: this.model,\n      max_tokens: maxTokens,\n      messages: [{ role: \"system\", content: system }, ...messages],\n      tools: openaiTools,\n      tool_choice: \"required\",\n    });\n\n    // openai v6 made tool_calls a union of function and custom calls; only the\n    // function variant carries `.function`.\n    const toolCall = response.choices[0]?.message?.tool_calls?.[0];\n    if (toolCall?.type === \"function\") {\n      return toolCall.function.arguments;\n    }\n\n    return response.choices[0]?.message?.content ?? \"\";\n  }\n\n  /**\n   * Produce a single embedding vector via the OpenAI embeddings API.\n   * Subclasses (e.g. Ollama) override embeddingModel() to pick a different model.\n   */\n  async embed(text: string): Promise<number[]> {\n    const response = await this.embeddingsClient.embeddings.create({\n      model: this.embeddingModel(),\n      input: text,\n    });\n\n    const vector = response.data[0]?.embedding;\n    if (!Array.isArray(vector)) {\n      throw new Error(\"OpenAI embeddings response did not include a vector.\");\n    }\n    return vector;\n  }\n\n  /** Default embedding model for this provider. Subclasses may override. */\n  protected embeddingModel(): string {\n    return this.configuredEmbeddingModel ?? EMBEDDING_MODELS.openai;\n  }\n}\n","/**\n * Ollama LLM provider implementation.\n *\n * Extends OpenAIProvider since Ollama exposes an OpenAI-compatible API.\n * Overrides only the constructor to set baseURL and disable API key auth.\n */\n\nimport { OpenAIProvider, readTimeoutEnv } from \"./openai.js\";\nimport { EMBEDDING_MODELS, OLLAMA_DEFAULT_TIMEOUT_MS } from \"../utils/constants.js\";\n\n/** Construction options for an Ollama-compatible provider. */\ninterface OllamaProviderOptions {\n  baseURL: string;\n  embeddingsBaseURL?: string;\n  embeddingModel?: string;\n  /**\n   * Per-request timeout in milliseconds. Defaults to 30 minutes for Ollama\n   * because local models on modest hardware can take much longer than the\n   * cloud-OpenAI default of 10. Override with OLLAMA_TIMEOUT_MS or the\n   * provider-agnostic LLMWIKI_REQUEST_TIMEOUT_MS env var.\n   */\n  timeoutMs?: number;\n}\n\n/** Resolve the Ollama timeout: explicit option → OLLAMA_TIMEOUT_MS → LLMWIKI_REQUEST_TIMEOUT_MS → default. */\nfunction resolveOllamaTimeoutMs(explicit?: number): number {\n  return (\n    explicit ??\n    readTimeoutEnv(\"OLLAMA_TIMEOUT_MS\") ??\n    readTimeoutEnv(\"LLMWIKI_REQUEST_TIMEOUT_MS\") ??\n    OLLAMA_DEFAULT_TIMEOUT_MS\n  );\n}\n\n/** Ollama-backed LLM provider using the OpenAI-compatible endpoint. */\nexport class OllamaProvider extends OpenAIProvider {\n  constructor(model: string, options: OllamaProviderOptions) {\n    super(model, {\n      baseURL: options.baseURL,\n      apiKey: \"ollama\",\n      embeddingsBaseURL: options.embeddingsBaseURL,\n      embeddingModel: options.embeddingModel,\n      timeoutMs: resolveOllamaTimeoutMs(options.timeoutMs),\n    });\n  }\n\n  /** Ollama ships a dedicated embedding model (nomic-embed-text). */\n  protected override embeddingModel(): string {\n    return this.configuredEmbeddingModel ?? EMBEDDING_MODELS.ollama;\n  }\n}\n","/**\n * MiniMax LLM provider implementation.\n *\n * Extends OpenAIProvider since MiniMax exposes an OpenAI-compatible API.\n * Overrides only the constructor to set MiniMax's base URL and API key.\n */\n\nimport { OpenAIProvider } from \"./openai.js\";\n\n/** MiniMax API base URL. */\nconst MINIMAX_BASE_URL = \"https://api.minimax.io/v1\";\n\n/** MiniMax-backed LLM provider using the OpenAI-compatible endpoint. */\nexport class MiniMaxProvider extends OpenAIProvider {\n  constructor(model: string, apiKey: string) {\n    super(model, { baseURL: MINIMAX_BASE_URL, apiKey });\n  }\n}\n","/**\n * GitHub Copilot LLM provider implementation.\n *\n * Uses the GitHub Copilot API (https://api.githubcopilot.com), which exposes\n * an OpenAI-compatible chat endpoint. Requires a GitHub OAuth token with\n * Copilot access — use `gh auth token` to obtain one. Classic PATs are NOT\n * supported by this endpoint.\n *\n * Note: GitHub Copilot does not expose an embeddings API. Calling embed() will\n * throw with a helpful message. For workflows that require semantic search\n * (query with chunked retrieval), use the openai provider with OPENAI_API_KEY.\n */\n\nimport { OpenAIProvider } from \"./openai.js\";\nimport { COPILOT_BASE_URL } from \"../utils/constants.js\";\n\n/** GitHub Copilot-backed LLM provider using the OpenAI-compatible endpoint. */\nexport class CopilotProvider extends OpenAIProvider {\n  constructor(model: string, apiKey: string) {\n    super(model, { baseURL: COPILOT_BASE_URL, apiKey });\n  }\n\n  /**\n   * GitHub Copilot has no native embeddings API.\n   * Throws an informative error directing the user to an alternative.\n   */\n  override async embed(_text: string): Promise<number[]> {\n    throw new Error(\n      \"GitHub Copilot does not support embeddings.\\n\" +\n      \"  For semantic search (llmwiki query), switch to the OpenAI provider:\\n\" +\n      \"    export LLMWIKI_PROVIDER=openai\\n\" +\n      \"    export OPENAI_API_KEY=sk-...\",\n    );\n  }\n}\n","/**\n * Claude Agent SDK LLM provider implementation.\n *\n * Wraps `@anthropic-ai/claude-agent-sdk`'s `query()` to implement the\n * LLMProvider interface. Unlike the `anthropic` provider (which calls the raw\n * Messages API), this backend routes through the Agent SDK and therefore\n * authenticates with the user's local Claude Code login (OAuth/subscription) —\n * no standalone ANTHROPIC_API_KEY is required.\n *\n * Generation runs in single-shot mode (one turn, no agentic file tools) so it\n * behaves like a plain completion. Structured output (`toolCall`) is handled\n * faithfully by registering the requested tool as an in-process SDK MCP tool\n * and capturing the model's `tool_use` input. Embeddings delegate to Voyage,\n * mirroring the `anthropic` provider.\n */\n\nimport { query, createSdkMcpServer, tool } from \"@anthropic-ai/claude-agent-sdk\";\nimport type { LLMProvider, LLMMessage, LLMTool } from \"../utils/provider.js\";\nimport { voyageEmbed } from \"./voyage-embed.js\";\nimport { jsonSchemaToZodShape } from \"./json-schema-to-zod.js\";\n\n/** Name for the throwaway in-process MCP server used to host a tool. */\nconst TOOL_SERVER_NAME = \"llmwiki\";\n\n/**\n * Turn ceiling for a single-shot request. The SDK reports an error result when\n * this ceiling is *reached*, so it must sit above the one turn a clean\n * completion or forced tool call actually consumes — `1` errors on every call.\n */\nconst MAX_TURNS = 4;\n\n/**\n * Appended to text-generation prompts. The Agent SDK runs an agentic model that\n * otherwise prefixes answers with conversational scaffolding (\"I'll write…\");\n * this keeps the output to the requested document, matching the raw API path.\n */\nconst OUTPUT_ONLY_DIRECTIVE =\n  \"Respond with only the requested content — no preamble, explanation, or sign-off.\";\n\n/** A content block on an assistant message (text or tool_use). */\ninterface AssistantBlock {\n  type: string;\n  text?: string;\n  name?: string;\n  input?: unknown;\n}\n\n/** Join the user-role message contents into a single prompt string. */\nfunction buildPrompt(messages: LLMMessage[]): string {\n  return messages.map((message) => message.content).join(\"\\n\\n\");\n}\n\n/** High-frequency SDK message types/subtypes that add noise without insight. */\nconst NOISY_MESSAGES = new Set([\"thinking_tokens\", \"rate_limit_event\"]);\n\n/** Resolve the LLMWIKI_DEBUG level: off, a concise trace, or the full SDK firehose. */\nfunction debugLevel(): \"off\" | \"on\" | \"verbose\" {\n  const value = process.env.LLMWIKI_DEBUG?.trim().toLowerCase();\n  if (!value) return \"off\";\n  return value === \"verbose\" || value === \"2\" ? \"verbose\" : \"on\";\n}\n\n/**\n * Extra query options that surface what the Agent SDK is doing. Always streams\n * the `claude` subprocess stderr when debugging; the full SDK verbose logs are\n * added only at the `verbose` level. Empty object unless LLMWIKI_DEBUG is set.\n */\nfunction debugOptions(): { debug?: boolean; stderr?: (data: string) => void } {\n  const level = debugLevel();\n  if (level === \"off\") return {};\n  return { debug: level === \"verbose\", stderr: (data) => process.stderr.write(data) };\n}\n\n/** Print a one-line trace of a meaningful SDK message (type and subtype). */\nfunction traceMessage(raw: unknown): void {\n  if (debugLevel() === \"off\") return;\n  const message = raw as { type?: string; subtype?: string };\n  if (NOISY_MESSAGES.has(message.subtype ?? \"\") || NOISY_MESSAGES.has(message.type ?? \"\")) return;\n  const subtype = message.subtype ? `:${message.subtype}` : \"\";\n  process.stderr.write(`[claude-agent] ${message.type ?? \"?\"}${subtype}\\n`);\n}\n\n/** Accumulate text from assistant content blocks, optionally emitting each chunk. */\nfunction accumulateText(blocks: AssistantBlock[], onToken?: (text: string) => void): string {\n  let text = \"\";\n  for (const block of blocks) {\n    if (block.type === \"text\" && block.text) {\n      text += block.text;\n      onToken?.(block.text);\n    }\n  }\n  return text;\n}\n\n/**\n * Extract the text of a success result, or throw on any error result subtype\n * (auth failure, max turns, execution failure, …). Failing loudly here keeps a\n * bad SDK run from silently producing empty or partial wiki output.\n */\nfunction resultText(message: { subtype?: string; result?: string; errors?: string[] }): string {\n  if (message.subtype === \"success\") return message.result ?? \"\";\n  const detail = message.errors?.join(\"; \") || message.subtype || \"unknown error\";\n  throw new Error(`Claude Agent SDK returned an error result: ${detail}`);\n}\n\n/** Return the input of the first matching `tool_use` block, or undefined. */\nfunction findToolInput(\n  blocks: AssistantBlock[],\n  toolName: string,\n  qualifiedName: string,\n): unknown {\n  const match = blocks.find(\n    (block) =>\n      block.type === \"tool_use\" && (block.name === toolName || block.name === qualifiedName),\n  );\n  return match?.input;\n}\n\n/** Claude Agent SDK-backed LLM provider using the local Claude Code login. */\nexport class ClaudeAgentProvider implements LLMProvider {\n  private readonly model: string;\n\n  constructor(model: string) {\n    this.model = model;\n  }\n\n  /** Send a single non-streaming completion request. */\n  async complete(system: string, messages: LLMMessage[], _maxTokens: number): Promise<string> {\n    return this.runText(system, buildPrompt(messages));\n  }\n\n  /** Stream a completion, invoking onToken for each text chunk. */\n  async stream(\n    system: string,\n    messages: LLMMessage[],\n    _maxTokens: number,\n    onToken?: (text: string) => void,\n  ): Promise<string> {\n    return this.runText(system, buildPrompt(messages), onToken);\n  }\n\n  /** Run a single-shot, tool-free query and accumulate the assistant's text. */\n  private async runText(\n    system: string,\n    prompt: string,\n    onToken?: (text: string) => void,\n  ): Promise<string> {\n    const response = query({\n      prompt,\n      options: {\n        systemPrompt: `${system}\\n\\n${OUTPUT_ONLY_DIRECTIVE}`,\n        model: this.model,\n        maxTurns: MAX_TURNS,\n        tools: [],\n        allowedTools: [],\n        ...debugOptions(),\n      },\n    });\n\n    let streamed = \"\";\n    let finalText = \"\";\n    for await (const message of response) {\n      traceMessage(message);\n      if (message.type === \"assistant\") {\n        streamed += accumulateText(message.message.content as AssistantBlock[], onToken);\n      } else if (message.type === \"result\") {\n        finalText = resultText(message);\n      }\n    }\n    return finalText || streamed;\n  }\n\n  /**\n   * Force a single structured tool call and return its input as a JSON string,\n   * matching the shape callers parse from the other providers.\n   */\n  async toolCall(\n    system: string,\n    messages: LLMMessage[],\n    tools: LLMTool[],\n    _maxTokens: number,\n  ): Promise<string> {\n    const requested = tools[0];\n    const qualifiedName = `mcp__${TOOL_SERVER_NAME}__${requested.name}`;\n    const sdkTool = tool(\n      requested.name,\n      requested.description,\n      jsonSchemaToZodShape(requested.input_schema),\n      async () => ({ content: [{ type: \"text\", text: \"ok\" }] }),\n    );\n    const mcpServer = createSdkMcpServer({ name: TOOL_SERVER_NAME, tools: [sdkTool] });\n\n    const response = query({\n      prompt: buildPrompt(messages),\n      options: {\n        systemPrompt: `${system}\\n\\nRespond by calling the \\`${requested.name}\\` tool.`,\n        model: this.model,\n        maxTurns: MAX_TURNS,\n        mcpServers: { [TOOL_SERVER_NAME]: mcpServer },\n        // Disable every built-in tool; only the in-process MCP tool is reachable.\n        tools: [],\n        allowedTools: [qualifiedName],\n        permissionMode: \"bypassPermissions\",\n        allowDangerouslySkipPermissions: true,\n        ...debugOptions(),\n      },\n    });\n    return collectToolInput(response, requested.name, qualifiedName);\n  }\n\n  /** Produce a single embedding vector via Voyage (Anthropic has no endpoint). */\n  async embed(text: string): Promise<number[]> {\n    return voyageEmbed(text);\n  }\n}\n\n/** An SDK message: assistant content, or a result whose error subtype must throw. */\ninterface StreamMessage {\n  type: string;\n  subtype?: string;\n  result?: string;\n  errors?: string[];\n  message?: { content: AssistantBlock[] };\n}\n\n/**\n * Read the first matching `tool_use` input from a query stream as JSON. Throws\n * on an SDK error result, and throws if the model never called the tool (prose\n * or empty output) — callers expect JSON, so a silent fallback would degrade\n * into zero extracted concepts or broken eval output.\n */\nasync function collectToolInput(\n  response: AsyncIterable<unknown>,\n  toolName: string,\n  qualifiedName: string,\n): Promise<string> {\n  let prose = \"\";\n  for await (const raw of response) {\n    traceMessage(raw);\n    const message = raw as StreamMessage;\n    if (message.type === \"result\") {\n      resultText(message); // throws on any error result; success is ignored here\n      continue;\n    }\n    if (message.type !== \"assistant\" || !message.message) continue;\n    const input = findToolInput(message.message.content, toolName, qualifiedName);\n    if (input !== undefined) return JSON.stringify(input);\n    prose += accumulateText(message.message.content);\n  }\n  const suffix = prose ? `; it responded with prose instead: ${prose.slice(0, 200)}` : \".\";\n  throw new Error(`Claude Agent SDK did not call the \"${toolName}\" tool${suffix}`);\n}\n","/**\n * Minimal JSON-Schema → Zod converter for the Claude Agent SDK.\n *\n * The Agent SDK's `tool()` helper takes a Zod *raw shape* (a record of Zod\n * types keyed by property name), but llmwiki declares its tools as JSON Schema\n * (`LLMTool.input_schema`). This converts the subset of JSON Schema that every\n * llmwiki tool uses — object / array / string / number / boolean / enum, with\n * a `required` list — into the raw shape the SDK expects. It is intentionally\n * narrow: unsupported nodes fall back to `z.unknown()` rather than throwing.\n *\n * Two contract details are preserved so the SDK path matches the raw API path:\n * numeric/boolean enums keep their literal types (e.g. eval scores `0 | 1 | 2`,\n * not `\"0\" | \"1\" | \"2\"`), and field `description`s carry through via `.describe`.\n */\n\nimport { z, type ZodType } from \"zod\";\n\n/** The slice of JSON Schema this converter understands. */\ninterface JsonSchemaNode {\n  type?: string;\n  properties?: Record<string, JsonSchemaNode>;\n  required?: string[];\n  items?: JsonSchemaNode;\n  enum?: unknown[];\n  description?: string;\n}\n\n/** Builders for primitive JSON Schema types, keyed by `type`. */\nconst SCALAR_BUILDERS: Record<string, () => ZodType> = {\n  string: () => z.string(),\n  number: () => z.number(),\n  integer: () => z.number(),\n  boolean: () => z.boolean(),\n};\n\n/** Build a Zod type for an enum, keeping numeric/boolean values as literals. */\nfunction enumToZod(values: unknown[]): ZodType {\n  if (values.every((value) => typeof value === \"string\")) {\n    return z.enum(values as [string, ...string[]]);\n  }\n  const literals = values.map((value) => z.literal(value as string | number | boolean));\n  return literals.length === 1\n    ? literals[0]\n    : z.union(literals as unknown as [ZodType, ZodType, ...ZodType[]]);\n}\n\n/** Map a JSON Schema node to a Zod type, ignoring any field description. */\nfunction baseType(node: JsonSchemaNode): ZodType {\n  if (Array.isArray(node.enum) && node.enum.length > 0) return enumToZod(node.enum);\n  const scalar = node.type ? SCALAR_BUILDERS[node.type] : undefined;\n  if (scalar) return scalar();\n  if (node.type === \"array\") {\n    return z.array(node.items ? nodeToZod(node.items) : z.unknown());\n  }\n  if (node.type === \"object\") return z.object(shapeFromProperties(node));\n  return z.unknown();\n}\n\n/** Convert a node to a Zod type, carrying its description through via .describe(). */\nfunction nodeToZod(node: JsonSchemaNode): ZodType {\n  const zodType = baseType(node);\n  return node.description ? zodType.describe(node.description) : zodType;\n}\n\n/** Build a Zod raw shape from an object schema's properties + required list. */\nfunction shapeFromProperties(schema: JsonSchemaNode): Record<string, ZodType> {\n  const properties = schema.properties ?? {};\n  const required = new Set(schema.required ?? []);\n  const shape: Record<string, ZodType> = {};\n  for (const [key, value] of Object.entries(properties)) {\n    const zodType = nodeToZod(value);\n    shape[key] = required.has(key) ? zodType : zodType.optional();\n  }\n  return shape;\n}\n\n/**\n * Convert an Anthropic-style tool `input_schema` (a JSON Schema object) into\n * the Zod raw shape accepted by the Agent SDK's `tool()` helper.\n */\nexport function jsonSchemaToZodShape(\n  inputSchema: Record<string, unknown>,\n): Record<string, ZodType> {\n  return shapeFromProperties(inputSchema as JsonSchemaNode);\n}\n","/**\n * LLM provider abstraction layer.\n *\n * Defines the LLMProvider interface and a factory function that reads\n * LLMWIKI_PROVIDER and LLMWIKI_MODEL env vars to instantiate the\n * appropriate backend (Anthropic, OpenAI, Ollama, or MiniMax).\n */\n\nimport { DEFAULT_PROVIDER, PROVIDER_MODELS, OLLAMA_DEFAULT_HOST } from \"./constants.js\";\nimport { AnthropicProvider } from \"../providers/anthropic.js\";\nimport { OpenAIProvider } from \"../providers/openai.js\";\nimport { OllamaProvider } from \"../providers/ollama.js\";\nimport { MiniMaxProvider } from \"../providers/minimax.js\";\nimport { CopilotProvider } from \"../providers/copilot.js\";\nimport { ClaudeAgentProvider } from \"../providers/claude-agent.js\";\nimport {\n  resolveAnthropicAuthFromEnv,\n  resolveAnthropicBaseURLFromEnv,\n  resolveAnthropicModelFromEnv,\n} from \"./claude-settings.js\";\n\n/** A single message in an LLM conversation. */\nexport interface LLMMessage {\n  role: \"user\" | \"assistant\";\n  content: string;\n}\n\n/** A tool definition in Anthropic-style format (used as the canonical shape). */\nexport interface LLMTool {\n  name: string;\n  description: string;\n  input_schema: Record<string, unknown>;\n}\n\n/** Provider-agnostic interface for LLM backends. */\nexport interface LLMProvider {\n  complete(system: string, messages: LLMMessage[], maxTokens: number): Promise<string>;\n  stream(\n    system: string,\n    messages: LLMMessage[],\n    maxTokens: number,\n    onToken?: (text: string) => void,\n  ): Promise<string>;\n  toolCall(\n    system: string,\n    messages: LLMMessage[],\n    tools: LLMTool[],\n    maxTokens: number,\n  ): Promise<string>;\n  /** Return a single embedding vector for the given text. */\n  embed(text: string): Promise<number[]>;\n}\n\nconst SUPPORTED_PROVIDERS: ReadonlySet<string> = new Set([\"anthropic\", \"claude-agent\", \"openai\", \"ollama\", \"minimax\", \"copilot\"]);\n\n/**\n * Factory that returns the appropriate LLMProvider based on env vars.\n * Reads LLMWIKI_PROVIDER (default \"anthropic\") and LLMWIKI_MODEL\n * (defaults per provider from PROVIDER_MODELS).\n *\n * Direct process.env access is acceptable here as this is a system boundary.\n */\nexport function getProvider(): LLMProvider {\n  const providerName = getProviderName();\n\n  switch (providerName) {\n    case \"anthropic\":\n      return getAnthropicProvider();\n    case \"claude-agent\":\n      return getClaudeAgentProvider();\n    case \"openai\":\n      return new OpenAIProvider(getModelForProvider(\"openai\"), {\n        baseURL: readOptionalEnv(\"OPENAI_BASE_URL\"),\n        embeddingsBaseURL: readOptionalEnv(\"OPENAI_EMBEDDINGS_BASE_URL\"),\n        embeddingModel: readOptionalEnv(\"LLMWIKI_EMBEDDING_MODEL\"),\n      });\n    case \"ollama\":\n      return new OllamaProvider(getModelForProvider(\"ollama\"), {\n        baseURL: readOptionalEnv(\"OLLAMA_HOST\") ?? OLLAMA_DEFAULT_HOST,\n        embeddingsBaseURL: readOptionalEnv(\"OLLAMA_EMBEDDINGS_HOST\"),\n        embeddingModel: readOptionalEnv(\"LLMWIKI_EMBEDDING_MODEL\"),\n      });\n    case \"minimax\":\n      return getMiniMaxProvider();\n    case \"copilot\":\n      return getCopilotProvider();\n    default:\n      throw new Error(`Unhandled provider: ${providerName}`);\n  }\n}\n\nfunction readOptionalEnv(name: string): string | undefined {\n  const value = process.env[name]?.trim();\n  return value ? value : undefined;\n}\n\nfunction getModelForProvider(providerName: \"openai\" | \"ollama\" | \"minimax\" | \"copilot\"): string {\n  return process.env.LLMWIKI_MODEL ?? PROVIDER_MODELS[providerName];\n}\n\nfunction getMiniMaxProvider(): MiniMaxProvider {\n  const apiKey = process.env.MINIMAX_API_KEY;\n  if (!apiKey) {\n    throw new Error(\n      \"MiniMax provider requires MINIMAX_API_KEY environment variable.\\n\" +\n      '  Set it with: export MINIMAX_API_KEY=your_key',\n    );\n  }\n  return new MiniMaxProvider(getModelForProvider(\"minimax\"), apiKey);\n}\n\nfunction getCopilotProvider(): CopilotProvider {\n  const apiKey = process.env.GITHUB_TOKEN;\n  if (!apiKey) {\n    throw new Error(\n      \"GitHub Copilot provider requires GITHUB_TOKEN environment variable.\\n\" +\n      \"  Run: gh auth refresh --scopes copilot\\n\" +\n      \"  Then set it with: export GITHUB_TOKEN=$(gh auth token)\\n\" +\n      \"  The token must belong to a GitHub account with an active Copilot subscription.\",\n    );\n  }\n  return new CopilotProvider(getModelForProvider(\"copilot\"), apiKey);\n}\n\nfunction getAnthropicProvider(): AnthropicProvider {\n  const model = resolveAnthropicModelFromEnv() ?? PROVIDER_MODELS.anthropic;\n  const baseURL = resolveAnthropicBaseURLFromEnv();\n  const auth = resolveAnthropicAuthFromEnv();\n\n  return new AnthropicProvider(model, {\n    baseURL,\n    ...auth,\n  });\n}\n\n/**\n * Build the Claude Agent SDK provider. Auth is handled by the local Claude Code\n * login, so no API key is read here; LLMWIKI_MODEL (or the Claude settings\n * model) still overrides the default model.\n */\nfunction getClaudeAgentProvider(): ClaudeAgentProvider {\n  const model = resolveAnthropicModelFromEnv() ?? PROVIDER_MODELS[\"claude-agent\"];\n  return new ClaudeAgentProvider(model);\n}\n\nfunction getProviderName(): string {\n  const providerName = process.env.LLMWIKI_PROVIDER ?? DEFAULT_PROVIDER;\n  if (!SUPPORTED_PROVIDERS.has(providerName)) {\n    throw new Error(\n      `Unknown provider \"${providerName}\". Supported: ${[...SUPPORTED_PROVIDERS].join(\", \")}`,\n    );\n  }\n  return providerName;\n}\n\n/** Expose the resolved provider name for callers that need model lookup. */\nexport function getActiveProviderName(): string {\n  return getProviderName();\n}\n\n/**\n * Resolve the model id the compile pipeline would call, without\n * instantiating a provider (which can require API credentials).\n *\n * Used by the export provenance stamp so a downstream auditor can tie a\n * compiled page back to the exact model that produced it. Mirrors the\n * per-provider model resolution in {@link getProvider} so the reported id\n * matches what an actual compile call would use.\n */\nexport function resolveActiveModelId(): string {\n  const providerName = getProviderName();\n  if (providerName === \"anthropic\") {\n    return resolveAnthropicModelFromEnv() ?? PROVIDER_MODELS.anthropic;\n  }\n  return getModelForProvider(providerName as \"openai\" | \"ollama\" | \"minimax\" | \"copilot\");\n}\n","/**\n * Shared LLM helper with provider abstraction.\n *\n * Provides callClaude() for backward compatibility — delegates to the\n * active LLMProvider while preserving retry logic with exponential backoff.\n * The provider is selected via LLMWIKI_PROVIDER env var (see provider.ts).\n */\n\nimport { RETRY_COUNT, RETRY_BASE_MS, RETRY_MULTIPLIER } from \"./constants.js\";\nimport { getProvider } from \"./provider.js\";\nimport type { LLMMessage, LLMTool } from \"./provider.js\";\nimport { note } from \"./output.js\";\n\n/** Sleep for a given number of milliseconds. */\nfunction sleep(ms: number): Promise<void> {\n  return new Promise((resolve) => setTimeout(resolve, ms));\n}\n\n// Matches 4xx status codes at the start of an error message, excluding 429\n// (rate-limit), which is transient and worth retrying.\nconst NON_RETRIABLE_RE = /^4(?!29)\\d\\d\\b/;\n\n/** Return true for client errors that will never succeed on retry (e.g. 401, 403). */\nfunction isNonRetriable(error: unknown): boolean {\n  const msg = error instanceof Error ? error.message : String(error);\n  return NON_RETRIABLE_RE.test(msg);\n}\n\ninterface CallClaudeOptions {\n  system: string;\n  messages: LLMMessage[];\n  tools?: LLMTool[];\n  maxTokens?: number;\n  stream?: boolean;\n  onToken?: (text: string) => void;\n}\n\n/**\n * Call the active LLM provider with retry logic.\n * Supports streaming, tool-use, and basic completion modes.\n * Preserves the original callClaude interface for backward compatibility.\n */\nexport async function callClaude(options: CallClaudeOptions): Promise<string> {\n  const { system, messages, tools, maxTokens = 4096, stream = false, onToken } = options;\n  const provider = getProvider();\n\n  for (let attempt = 0; attempt <= RETRY_COUNT; attempt++) {\n    try {\n      if (stream) {\n        return await provider.stream(system, messages, maxTokens, onToken);\n      }\n\n      if (tools && tools.length > 0) {\n        return await provider.toolCall(system, messages, tools, maxTokens);\n      }\n\n      return await provider.complete(system, messages, maxTokens);\n    } catch (error) {\n      if (attempt === RETRY_COUNT || isNonRetriable(error)) throw error;\n\n      const delayMs = RETRY_BASE_MS * Math.pow(RETRY_MULTIPLIER, attempt);\n      const errMsg = error instanceof Error ? error.message : String(error);\n      note(`⚠ API call failed (attempt ${attempt + 1}/${RETRY_COUNT + 1}): ${errMsg}`);\n      note(`  Retrying in ${delayMs / 1000}s...`);\n      await sleep(delayMs);\n    }\n  }\n\n  throw new Error(\"Unreachable\");\n}\n","/**\n * PID-based lock file for preventing concurrent compilation.\n *\n * Fresh acquisition uses O_CREAT | O_EXCL (the 'wx' flag) for atomic lock\n * creation — the kernel guarantees only one process can create the file.\n *\n * Stale lock reclamation uses a two-lock protocol:\n * 1. Acquire a reclamation lock (.llmwiki/lock.reclaim) via 'wx' to serialize\n *    all processes attempting to reclaim the same stale main lock.\n * 2. Re-verify the main lock is still stale (another reclaimer may have\n *    already fixed it).\n * 3. unlink + tryCreateLock('wx') on the main lock — safe because we hold\n *    exclusive reclamation access.\n * 4. Release the reclamation lock in a finally block.\n *\n * The reclamation lock itself can become stale if a process crashes during\n * the brief reclamation window. When that happens, acquireReclaimLock only\n * cleans up the stale file — it does NOT retry acquisition in the same call.\n * This eliminates the unlink-then-create race that would allow two processes\n * to both hold the reclaim lock. The outer retry loop in acquireLock handles\n * convergence: first pass cleans up the stale reclaim lock, second pass\n * acquires it cleanly via 'wx'.\n */\n\nimport { open, readFile, unlink, mkdir } from \"fs/promises\";\nimport path from \"path\";\nimport { LLMWIKI_DIR, LOCK_FILE } from \"./constants.js\";\nimport * as output from \"./output.js\";\n\nconst RECLAIM_SUFFIX = \".reclaim\";\nconst MAX_ACQUIRE_ATTEMPTS = 2;\n\n/** Check whether a process with the given PID is still running. */\nfunction isProcessAlive(pid: number): boolean {\n  try {\n    process.kill(pid, 0);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Acquire the compilation lock. Returns true if acquired, false if busy.\n *\n * Retries up to MAX_ACQUIRE_ATTEMPTS times to handle the case where the\n * first attempt cleans up a stale reclamation lock but cannot acquire it\n * in the same call (to avoid the double-winner race).\n */\nexport async function acquireLock(root: string): Promise<boolean> {\n  const lockPath = path.join(root, LOCK_FILE);\n  await mkdir(path.join(root, LLMWIKI_DIR), { recursive: true });\n\n  for (let attempt = 0; attempt < MAX_ACQUIRE_ATTEMPTS; attempt++) {\n    // Try atomic create — fails if file already exists\n    const created = await tryCreateLock(lockPath);\n    if (created) return true;\n\n    // Lock exists. Check if the holding process is dead.\n    const stale = await isLockStale(lockPath);\n    if (!stale) {\n      output.status(\"!\", output.warn(\"Another compilation is running.\"));\n      return false;\n    }\n\n    // Stale lock — serialize reclamation via a second lock.\n    const reclaimed = await reclaimStaleLock(root, lockPath);\n    if (reclaimed) return true;\n\n    // Reclamation failed (e.g. cleaned up stale reclaim lock). Retry.\n  }\n\n  output.status(\"!\", output.warn(\"Could not acquire lock after retrying.\"));\n  return false;\n}\n\n/**\n * Reclaim a stale main lock using a serialized two-lock protocol.\n *\n * Acquires .llmwiki/lock.reclaim (via 'wx') so that only one process performs\n * the unlink + recreate sequence at a time. Re-verifies staleness under\n * the reclamation lock in case another process already fixed it.\n * @param root - Project root directory.\n * @param lockPath - Absolute path to the main lock file.\n */\nasync function reclaimStaleLock(root: string, lockPath: string): Promise<boolean> {\n  const reclaimPath = lockPath + RECLAIM_SUFFIX;\n\n  const gotReclaimLock = await acquireReclaimLock(reclaimPath);\n  if (!gotReclaimLock) return false;\n\n  try {\n    // Re-verify under exclusive reclamation access.\n    // Another reclaimer may have already fixed the main lock.\n    if (!(await isLockStale(lockPath))) {\n      return false;\n    }\n\n    // Still stale. Safe to reclaim — we're the only reclaimer.\n    try { await unlink(lockPath); } catch { /* already gone */ }\n\n    const acquired = await tryCreateLock(lockPath);\n    if (acquired) {\n      output.status(\"i\", output.dim(\"Reclaimed stale lock from dead process.\"));\n    }\n    return acquired;\n  } finally {\n    try { await unlink(reclaimPath); } catch { /* cleanup best-effort */ }\n  }\n}\n\n/**\n * Acquire the reclamation lock. Uses 'wx' for atomic creation.\n *\n * If the reclaim lock is stale (holder crashed during reclamation), this\n * function ONLY cleans up the stale file and returns false. It does NOT\n * retry acquisition in the same call. This is the key safety property:\n * unlink and create never happen in the same call, so two processes that\n * both see a stale reclaim lock will both clean up (harmless — second\n * unlink gets ENOENT) and both return false. Neither holds the reclaim\n * lock, so neither proceeds to touch the main lock. The outer retry loop\n * in acquireLock converges on the next attempt via a clean 'wx'.\n * @param reclaimPath - Absolute path to the reclamation lock file.\n */\nasync function acquireReclaimLock(reclaimPath: string): Promise<boolean> {\n  if (await tryCreateLock(reclaimPath)) return true;\n\n  // Reclaim lock exists. If its holder is alive, back off.\n  if (!(await isLockStale(reclaimPath))) return false;\n\n  // Stale reclaim lock — clean it up but do NOT retry in this call.\n  // Retrying here would reintroduce the unlink+create race.\n  try { await unlink(reclaimPath); } catch { /* already gone */ }\n  return false;\n}\n\n/**\n * Atomically create the lock file with our PID.\n * Returns true if we created it, false if it already exists.\n */\nasync function tryCreateLock(lockPath: string): Promise<boolean> {\n  try {\n    const fd = await open(lockPath, \"wx\");\n    await fd.writeFile(String(process.pid), \"utf-8\");\n    await fd.close();\n    return true;\n  } catch (err: unknown) {\n    if (err instanceof Error && \"code\" in err && (err as NodeJS.ErrnoException).code === \"EEXIST\") {\n      return false;\n    }\n    throw err;\n  }\n}\n\n/** Check if an existing lock is stale (holding process is dead). */\nasync function isLockStale(lockPath: string): Promise<boolean> {\n  try {\n    const content = await readFile(lockPath, \"utf-8\");\n    const pid = parseInt(content.trim(), 10);\n    if (isNaN(pid)) return true;\n    return !isProcessAlive(pid);\n  } catch {\n    return true;\n  }\n}\n\n/** Release the compilation lock. Safe to call even if lock doesn't exist. */\nexport async function releaseLock(root: string): Promise<void> {\n  const lockPath = path.join(root, LOCK_FILE);\n  try {\n    await unlink(lockPath);\n  } catch {\n    // Lock already removed or never existed\n  }\n}\n","/**\n * Output-language configuration for LLM-generated wiki content (issue #37).\n *\n * Resolves the user's chosen target language for compile and query\n * prompts. The CLI's `--lang <code>` flag and the `LLMWIKI_OUTPUT_LANG`\n * environment variable both write into the same env slot, so prompt\n * builders only need to read one source of truth.\n *\n * When unset, the resolver returns null — preserving the historical\n * behaviour where the LLM follows its own default (typically the\n * source-document language, often English).\n */\n\nconst LANG_ENV_VAR = \"LLMWIKI_OUTPUT_LANG\";\n\n/**\n * Read the configured output language. Returns null when the user has\n * not opted into a specific target language.\n */\nexport function getOutputLanguage(): string | null {\n  const raw = process.env[LANG_ENV_VAR];\n  if (!raw) return null;\n  const trimmed = raw.trim();\n  return trimmed.length > 0 ? trimmed : null;\n}\n\n/**\n * Build the language-directive line to inject into a system prompt.\n * Returns an empty string when no language is configured, which lets\n * callers concatenate unconditionally without producing an extra blank\n * line in the default case.\n */\nexport function languageDirective(): string {\n  const lang = getOutputLanguage();\n  if (!lang) return \"\";\n  return `Write the output in ${lang}.`;\n}\n\n/**\n * Apply a CLI `--lang <code>` value into the shared env slot so prompt\n * builders pick it up downstream. No-op when the caller did not pass the\n * flag. Trims whitespace so accidental padding does not leak into the\n * language directive.\n *\n * Lives in this module (not cli.ts) so every CLI verb plus the upcoming\n * quickstart command share one implementation and the resolution order\n * cannot drift between them.\n */\nexport function applyLanguageOption(lang: string | undefined): void {\n  if (lang && lang.trim().length > 0) {\n    process.env.LLMWIKI_OUTPUT_LANG = lang.trim();\n  }\n}\n","/**\n * LLM prompt templates and tool schemas for the compilation pipeline.\n * Contains the Anthropic tool definition for concept extraction,\n * prompt builders for both extraction and page generation phases,\n * and a parser for the structured tool output.\n */\n\nimport type {\n  ContradictionRef,\n  ExtractedConcept,\n  ProvenanceState,\n} from \"../utils/types.js\";\nimport type { PageKindRule, SeedPage } from \"../schema/index.js\";\nimport { languageDirective } from \"../utils/output-language.js\";\n\n/**\n * Build a list of optional prompt lines, omitting empty entries so the\n * default-case prompt is byte-identical to the previous version. Used by\n * the prompt builders to splice in the output-language directive only\n * when the user opted in.\n */\nfunction withLangLine(...lines: string[]): string[] {\n  const lang = languageDirective();\n  return lang ? [...lines, lang] : lines;\n}\n\n/**\n * Named version of the extraction + page-generation prompt contract.\n *\n * Bump this whenever the wording of the extraction tool schema, the\n * extraction system prompt, or the page-generation prompt changes in a way\n * that could alter compiled page content. The export provenance stamp\n * (`promptVersion` in the JSON export envelope) carries this value so a\n * downstream auditor can distinguish pages produced under different prompt\n * generations even when the model id is identical. Format is `vMAJOR`.\n */\nexport const PROMPT_VERSION = \"v1\";\n\n/** Allowed provenance state strings emitted by the LLM tool schema. */\nconst PROVENANCE_STATE_VALUES: ProvenanceState[] = [\n  \"extracted\",\n  \"merged\",\n  \"inferred\",\n  \"ambiguous\",\n];\n\n/**\n * Anthropic Tool definition for extracting knowledge concepts from a source.\n * Used with callClaude's tool_use mode to get structured concept data.\n */\nexport const CONCEPT_EXTRACTION_TOOL = {\n  name: \"extract_concepts\",\n  description: \"Extract knowledge concepts from a source document\",\n  input_schema: {\n    type: \"object\" as const,\n    properties: {\n      concepts: {\n        type: \"array\",\n        items: {\n          type: \"object\",\n          properties: {\n            concept: {\n              type: \"string\",\n              description: \"Human-readable concept title\",\n            },\n            summary: {\n              type: \"string\",\n              description: \"One-line description\",\n            },\n            is_new: {\n              type: \"boolean\",\n              description: \"True if this is a new concept not in existing wiki\",\n            },\n            tags: {\n              type: \"array\",\n              items: { type: \"string\" },\n              description:\n                \"2-4 categorical tags for organizing this concept (e.g., 'machine-learning', 'optimization')\",\n            },\n            confidence: {\n              type: \"number\",\n              description:\n                \"Confidence in this concept on a 0..1 scale (1 = directly stated, 0 = highly speculative).\",\n            },\n            provenance_state: {\n              type: \"string\",\n              enum: PROVENANCE_STATE_VALUES,\n              description:\n                \"How this concept was produced: 'extracted' (direct from source), 'merged' (synthesised across sources), 'inferred' (model deduction), or 'ambiguous' (sources disagree).\",\n            },\n            contradicted_by: {\n              type: \"array\",\n              items: {\n                type: \"object\",\n                properties: {\n                  slug: { type: \"string\", description: \"Slug of the contradicting concept.\" },\n                  reason: { type: \"string\", description: \"Brief reason for the contradiction.\" },\n                },\n                required: [\"slug\"],\n              },\n              description: \"Slugs of other concepts whose evidence contradicts this one.\",\n            },\n          },\n          required: [\"concept\", \"summary\", \"is_new\"],\n        },\n      },\n    },\n    required: [\"concepts\"],\n  },\n};\n\n/**\n * Build the system prompt for the concept extraction phase.\n * Instructs the LLM to analyze a source document and identify distinct concepts.\n * @param sourceContent - The full text of the source document.\n * @param existingIndex - The current wiki index.md contents (may be empty).\n * @returns System prompt string for the extraction call.\n */\nexport function buildExtractionPrompt(\n  sourceContent: string,\n  existingIndex: string,\n): string {\n  const indexSection = existingIndex\n    ? `\\n\\nHere is the existing wiki index — avoid duplicating concepts already covered:\\n\\n${existingIndex}`\n    : \"\\n\\nNo existing wiki pages yet.\";\n\n  return [\n    ...withLangLine(\n      \"You are a knowledge extraction engine. Analyze the following source document\",\n      \"and identify 3-8 distinct, meaningful concepts worth documenting as wiki pages.\",\n      \"Each concept should be a standalone topic that someone might look up.\",\n      \"Focus on key ideas, techniques, patterns, or entities — not trivial details.\",\n      \"Use the extract_concepts tool to return your findings.\",\n    ),\n    \"\",\n    \"For every concept, emit provenance metadata so downstream tools can reason\",\n    \"about reliability:\",\n    \"  - confidence: 0..1 — how certain you are the source supports this concept.\",\n    \"  - provenance_state: 'extracted' if directly stated, 'merged' if synthesised\",\n    \"    from multiple parts of the source, 'inferred' if reasoned from context,\",\n    \"    or 'ambiguous' if the source is contradictory or unclear.\",\n    \"  - contradicted_by: slugs of other concepts (in this batch or the index)\",\n    \"    whose evidence conflicts with this one.\",\n    indexSection,\n    \"\\n\\n--- SOURCE DOCUMENT ---\\n\\n\",\n    sourceContent,\n  ].join(\"\\n\");\n}\n\n/**\n * Build the system prompt for wiki page generation.\n * Instructs the LLM to write a complete wiki page for a single concept.\n * @param concept - The concept title to write about.\n * @param sourceContent - The source material to draw from.\n * @param existingPage - The current page content if updating (empty for new pages).\n * @param relatedPages - Concatenated content of related wiki pages for context.\n * @returns System prompt string for the page generation call.\n */\nexport function buildPagePrompt(\n  concept: string,\n  sourceContent: string,\n  existingPage: string,\n  relatedPages: string,\n): string {\n  const existingSection = existingPage\n    ? `\\n\\nExisting page to update:\\n\\n${existingPage}`\n    : \"\";\n\n  const relatedSection = relatedPages\n    ? `\\n\\nRelated wiki pages for cross-referencing:\\n\\n${relatedPages}`\n    : \"\";\n\n  return [\n    ...withLangLine(\n      `You are a wiki author. Write a clear, well-structured markdown page about \"${concept}\".`,\n      \"Draw facts only from the provided source material.\",\n      \"Include a ## Sources section at the end listing the source document.\",\n      \"Suggest [[wikilinks]] to related concepts where appropriate.\",\n      \"Write in a neutral, informative tone. Be concise but thorough.\",\n    ),\n    \"\",\n    \"Source attribution: at the end of each prose paragraph, append a citation\",\n    \"marker identifying which source file(s) and line range the paragraph drew from.\",\n    \"PREFERRED format: ^[filename.md:START-END] where START and END are the line numbers\",\n    \"shown in the numbered source content below (e.g. ' 42 | some text' → line 42).\",\n    \"Use this whenever you can identify the specific numbered lines supporting the claim.\",\n    \"Fallback format: ^[filename.md] when the claim draws from the source broadly and\",\n    \"no specific line range applies. For multi-source paragraphs: ^[a.md:1-5, b.md:10-12].\",\n    \"Place citations only at the end of prose paragraphs or sentences — not on\",\n    \"headings, list items, or code blocks.\",\n    \"Do not cite YAML frontmatter lines (the --- ... --- block at the top of a file) as\",\n    \"source evidence for substantive claims — those lines are metadata, not content.\",\n    \"If a claim relates to a metadata field (e.g. document date or author), leave it uncited.\",\n    \"Source filenames are visible as `--- SOURCE: filename.md ---` headers in the content below.\",\n    \"\",\n    \"If a paragraph is your inference rather than a direct extraction, leave it\",\n    \"uncited — downstream lint rules will count uncited paragraphs as 'inferred'\",\n    \"so lint can surface excess-inferred-paragraphs warnings on review.\",\n    existingSection,\n    relatedSection,\n    \"\\n\\n--- SOURCE MATERIAL ---\\n\\n\",\n    sourceContent,\n  ].join(\"\\n\");\n}\n\n/** Raw concept shape as it arrives from the tool JSON. */\ninterface RawConcept {\n  concept: unknown;\n  summary: unknown;\n  is_new: unknown;\n  tags?: unknown;\n  confidence?: unknown;\n  provenance_state?: unknown;\n  contradicted_by?: unknown;\n}\n\n/** True if the raw concept has the required string/boolean fields. */\nfunction isValidRawConcept(c: RawConcept): boolean {\n  return (\n    typeof c.concept === \"string\" &&\n    typeof c.summary === \"string\" &&\n    typeof c.is_new === \"boolean\" &&\n    (c.tags === undefined || Array.isArray(c.tags))\n  );\n}\n\n/** Coerce raw contradiction entries from the tool into typed refs. */\nfunction coerceContradictedBy(raw: unknown): ContradictionRef[] | undefined {\n  if (!Array.isArray(raw)) return undefined;\n  const refs: ContradictionRef[] = [];\n  for (const entry of raw) {\n    if (!entry || typeof entry !== \"object\") continue;\n    const obj = entry as { slug?: unknown; reason?: unknown };\n    if (typeof obj.slug !== \"string\" || obj.slug.trim().length === 0) continue;\n    const ref: ContradictionRef = { slug: obj.slug.trim() };\n    if (typeof obj.reason === \"string\") ref.reason = obj.reason;\n    refs.push(ref);\n  }\n  return refs.length > 0 ? refs : undefined;\n}\n\n/** Map a validated raw concept into an ExtractedConcept. */\nfunction mapRawConcept(c: RawConcept): ExtractedConcept {\n  const provenance = typeof c.provenance_state === \"string\" &&\n    PROVENANCE_STATE_VALUES.includes(c.provenance_state as ProvenanceState)\n    ? (c.provenance_state as ProvenanceState)\n    : undefined;\n  return {\n    concept: c.concept as string,\n    summary: c.summary as string,\n    is_new: c.is_new as boolean,\n    tags: Array.isArray(c.tags) ? (c.tags as string[]) : undefined,\n    confidence: typeof c.confidence === \"number\" ? c.confidence : undefined,\n    provenanceState: provenance,\n    contradictedBy: coerceContradictedBy(c.contradicted_by),\n  };\n}\n\n/**\n * Build a system prompt for generating a seed page (overview / comparison /\n * entity) declared in the project's schema config. Seed pages weave together\n * material from related concept pages rather than from raw source files.\n * @param seed - Seed page definition pulled from the schema.\n * @param rule - Per-kind rule (used for the description and link minimum).\n * @param relatedPagesContent - Concatenated content of related concept pages.\n * @returns System prompt string for the page generation call.\n */\nexport function buildSeedPagePrompt(\n  seed: SeedPage,\n  rule: PageKindRule,\n  relatedPagesContent: string,\n): string {\n  const minLinks = rule.minWikilinks;\n  const linkExpectation = minLinks > 0\n    ? `Include at least ${minLinks} [[wikilinks]] to related pages.`\n    : \"Use [[wikilinks]] when referencing other pages.\";\n  return [\n    ...withLangLine(\n      `You are a wiki author. Write a ${seed.kind} page titled \"${seed.title}\".`,\n      `Page-kind guidance: ${rule.description}`,\n      `Summary line for context: ${seed.summary}`,\n      \"Draw facts only from the related wiki pages provided below.\",\n      linkExpectation,\n      \"Write in a neutral, informative tone. Be concise but thorough.\",\n    ),\n    \"\\n\\n--- RELATED PAGES ---\\n\\n\",\n    relatedPagesContent,\n  ].join(\"\\n\");\n}\n\n/**\n * Parse the JSON tool output from concept extraction into typed objects.\n * @param toolOutput - Raw JSON string returned from the extract_concepts tool.\n * @returns Array of ExtractedConcept objects.\n */\nexport function parseConcepts(toolOutput: string): ExtractedConcept[] {\n  try {\n    const parsed = JSON.parse(toolOutput);\n    const concepts: RawConcept[] = parsed.concepts ?? [];\n    return concepts.filter(isValidRawConcept).map(mapRawConcept);\n  } catch {\n    return [];\n  }\n}\n","/**\n * Type definitions for the wiki schema layer.\n *\n * The schema layer turns llmwiki from a flat compiler pipeline into a shaped\n * knowledge system. It declares the kinds of pages a project supports\n * (`concept`, `entity`, `comparison`, `overview`) and the cross-link\n * expectations that lint and review enforce per kind.\n *\n * Types live in their own module so that compile, lint, CLI, and tests can\n * depend on the schema vocabulary without pulling in YAML/JSON loaders.\n */\n\n/** All page kinds the schema layer recognises. */\nexport type PageKind = \"concept\" | \"entity\" | \"comparison\" | \"overview\";\n\n/** All recognised page kinds, exported for validation and CLI display. */\nexport const PAGE_KINDS: readonly PageKind[] = [\n  \"concept\",\n  \"entity\",\n  \"comparison\",\n  \"overview\",\n] as const;\n\n/** Per-kind policy: minimum cross-links and a human description used in prompts. */\nexport interface PageKindRule {\n  /** Minimum number of [[wikilinks]] a page of this kind should contain. */\n  minWikilinks: number;\n  /** Short human-readable description; surfaced in prompts and review output. */\n  description: string;\n}\n\n/** Optional declarative seed for non-concept pages the compiler can generate. */\nexport interface SeedPage {\n  /** Display title; also used to derive the page slug. */\n  title: string;\n  /** Page kind — must be one of `PAGE_KINDS`. */\n  kind: PageKind;\n  /** One-line summary written into frontmatter. */\n  summary: string;\n  /**\n   * For `overview` and `comparison` kinds, the slugs the page should weave\n   * together. The compiler passes these to the LLM as the source material.\n   */\n  relatedSlugs?: string[];\n}\n\n/** Resolved schema config the rest of the compiler reads. */\nexport interface SchemaConfig {\n  /** Schema format version. Currently always `1`. */\n  version: 1;\n  /** Kind assigned to pages that don't declare a kind in frontmatter. */\n  defaultKind: PageKind;\n  /** Per-kind rules keyed by `PageKind`. */\n  kinds: Record<PageKind, PageKindRule>;\n  /** Optional seed pages the compiler should materialise on each run. */\n  seedPages: SeedPage[];\n  /** Path the schema was loaded from, or `null` when defaults are used. */\n  loadedFrom: string | null;\n}\n\n/** Raw schema file contents — every field is optional so partial files work. */\nexport interface PartialSchemaFile {\n  version?: number;\n  defaultKind?: string;\n  kinds?: Partial<Record<string, Partial<PageKindRule>>>;\n  seedPages?: Array<Partial<SeedPage>>;\n}\n","/**\n * Default schema constants.\n *\n * Projects without a schema file fall back to these defaults so the compiler\n * keeps working on day one. Every existing wiki — created before the schema\n * layer existed — is treated as a wiki of `concept` pages with no\n * cross-link minimums, preserving backward compatibility.\n */\n\nimport type { PageKind, PageKindRule, SchemaConfig } from \"./types.js\";\n\n/** Minimum cross-links per kind, chosen to match each kind's purpose. */\nconst DEFAULT_MIN_LINKS: Record<PageKind, number> = {\n  concept: 0,\n  entity: 1,\n  comparison: 2,\n  overview: 3,\n};\n\n/** Human-readable descriptions used in prompts and review output. */\nconst DEFAULT_DESCRIPTIONS: Record<PageKind, string> = {\n  concept: \"A standalone idea, technique, or pattern worth documenting.\",\n  entity: \"A specific thing — a person, product, organization, or named artifact.\",\n  comparison: \"A side-by-side analysis weighing two or more concepts or entities.\",\n  overview: \"A top-down map page that situates several concepts within a domain.\",\n};\n\n/** Build the default per-kind rule table. */\nfunction buildDefaultKindRules(): Record<PageKind, PageKindRule> {\n  return {\n    concept: { minWikilinks: DEFAULT_MIN_LINKS.concept, description: DEFAULT_DESCRIPTIONS.concept },\n    entity: { minWikilinks: DEFAULT_MIN_LINKS.entity, description: DEFAULT_DESCRIPTIONS.entity },\n    comparison: {\n      minWikilinks: DEFAULT_MIN_LINKS.comparison,\n      description: DEFAULT_DESCRIPTIONS.comparison,\n    },\n    overview: {\n      minWikilinks: DEFAULT_MIN_LINKS.overview,\n      description: DEFAULT_DESCRIPTIONS.overview,\n    },\n  };\n}\n\n/** The schema returned when no schema file exists. */\nexport function buildDefaultSchema(): SchemaConfig {\n  return {\n    version: 1,\n    defaultKind: \"concept\",\n    kinds: buildDefaultKindRules(),\n    seedPages: [],\n    loadedFrom: null,\n  };\n}\n","/**\n * Schema config loader.\n *\n * Discovers a project's schema file from a fixed list of candidate paths,\n * parses it (JSON or YAML), and merges it onto the default schema. Missing\n * files are not an error — the compiler falls back to defaults so existing\n * projects continue to work without any migration.\n */\n\nimport { existsSync } from \"fs\";\nimport { readFile } from \"fs/promises\";\nimport path from \"path\";\nimport yaml from \"js-yaml\";\nimport type {\n  PageKind,\n  PageKindRule,\n  PartialSchemaFile,\n  SchemaConfig,\n  SeedPage,\n} from \"./types.js\";\nimport { PAGE_KINDS } from \"./types.js\";\nimport { buildDefaultSchema } from \"./defaults.js\";\n\n/** Candidate schema file paths searched in priority order. */\nconst SCHEMA_CANDIDATE_PATHS = [\n  \".llmwiki/schema.json\",\n  \".llmwiki/schema.yaml\",\n  \".llmwiki/schema.yml\",\n  \"wiki/.schema.yaml\",\n  \"wiki/.schema.yml\",\n];\n\n/** Find the first existing schema candidate path under `root`, or null. */\nfunction findSchemaPath(root: string): string | null {\n  for (const candidate of SCHEMA_CANDIDATE_PATHS) {\n    const absolute = path.join(root, candidate);\n    if (existsSync(absolute)) return absolute;\n  }\n  return null;\n}\n\n/** Decide whether to parse the file as JSON or YAML based on its extension. */\nfunction parseSchemaFile(filePath: string, content: string): PartialSchemaFile {\n  const isJson = filePath.endsWith(\".json\");\n  const parsed = isJson ? JSON.parse(content) : yaml.load(content);\n  if (parsed && typeof parsed === \"object\") return parsed as PartialSchemaFile;\n  return {};\n}\n\n/** Type-guard checking whether a string is one of the supported page kinds. */\nfunction isPageKind(value: unknown): value is PageKind {\n  return typeof value === \"string\" && (PAGE_KINDS as readonly string[]).includes(value);\n}\n\n/** Merge a single per-kind rule from the file onto the default rule. */\nfunction mergeKindRule(\n  defaults: PageKindRule,\n  override: Partial<PageKindRule> | undefined,\n): PageKindRule {\n  if (!override) return defaults;\n  const minWikilinks = typeof override.minWikilinks === \"number\"\n    ? override.minWikilinks\n    : defaults.minWikilinks;\n  const description = typeof override.description === \"string\"\n    ? override.description\n    : defaults.description;\n  return { minWikilinks, description };\n}\n\n/** Merge per-kind rule overrides onto the default rule table. */\nfunction mergeKinds(\n  defaults: Record<PageKind, PageKindRule>,\n  overrides: PartialSchemaFile[\"kinds\"],\n): Record<PageKind, PageKindRule> {\n  const merged = { ...defaults };\n  if (!overrides) return merged;\n\n  for (const kind of PAGE_KINDS) {\n    merged[kind] = mergeKindRule(defaults[kind], overrides[kind]);\n  }\n  return merged;\n}\n\n/** Validate and coerce a single seed page entry. Returns null when invalid. */\nfunction normalizeSeedPage(entry: Partial<SeedPage>): SeedPage | null {\n  if (typeof entry.title !== \"string\" || entry.title.trim() === \"\") return null;\n  if (!isPageKind(entry.kind)) return null;\n  const summary = typeof entry.summary === \"string\" ? entry.summary : \"\";\n  const relatedSlugs = Array.isArray(entry.relatedSlugs)\n    ? entry.relatedSlugs.filter((slug): slug is string => typeof slug === \"string\")\n    : undefined;\n  return { title: entry.title, kind: entry.kind, summary, relatedSlugs };\n}\n\n/** Coerce raw seed page entries into validated SeedPage objects. */\nfunction normalizeSeedPages(entries: PartialSchemaFile[\"seedPages\"]): SeedPage[] {\n  if (!Array.isArray(entries)) return [];\n  return entries\n    .map(normalizeSeedPage)\n    .filter((entry): entry is SeedPage => entry !== null);\n}\n\n/** Apply a parsed partial-schema onto the defaults, returning the resolved config. */\nfunction applyOverrides(\n  defaults: SchemaConfig,\n  overrides: PartialSchemaFile,\n  loadedFrom: string,\n): SchemaConfig {\n  const defaultKind = isPageKind(overrides.defaultKind)\n    ? overrides.defaultKind\n    : defaults.defaultKind;\n  return {\n    version: 1,\n    defaultKind,\n    kinds: mergeKinds(defaults.kinds, overrides.kinds),\n    seedPages: normalizeSeedPages(overrides.seedPages),\n    loadedFrom,\n  };\n}\n\n/**\n * Load the schema for `root`, falling back to defaults when no file is present.\n * Throws on parse failure so the user sees a clear error rather than a silent\n * default — silent fallback would mask real config bugs.\n * @param root - Project root directory.\n * @returns Resolved schema config.\n */\nexport async function loadSchema(root: string): Promise<SchemaConfig> {\n  const defaults = buildDefaultSchema();\n  const schemaPath = findSchemaPath(root);\n  if (!schemaPath) return defaults;\n\n  const raw = await readFile(schemaPath, \"utf-8\");\n  const parsed = parseSchemaFile(schemaPath, raw);\n  return applyOverrides(defaults, parsed, schemaPath);\n}\n\n/** Expose candidate paths so the CLI `schema init` command can pick one. */\nexport function defaultSchemaInitPath(root: string): string {\n  return path.join(root, SCHEMA_CANDIDATE_PATHS[0]);\n}\n","/**\n * Schema helper utilities shared by compile, lint, and CLI.\n *\n * Kept separate from `loader.ts` so callers that just need to interpret a\n * page's kind or count its wikilinks don't pull the YAML/JSON parser into\n * their dependency graph.\n */\n\nimport yaml from \"js-yaml\";\nimport type { PageKind, SchemaConfig } from \"./types.js\";\nimport { PAGE_KINDS } from \"./types.js\";\n\n/** Pattern matching [[Wikilink Title]] references in markdown content. */\nconst WIKILINK_PATTERN = /\\[\\[([^\\]]+)\\]\\]/g;\n\n/**\n * Resolve a page's kind from its raw frontmatter value, falling back to the\n * schema default when no explicit kind is set or the value is invalid.\n * @param rawKind - Raw `kind` value pulled from frontmatter (untyped).\n * @param schema - Resolved schema config.\n * @returns The resolved page kind.\n */\nexport function resolvePageKind(rawKind: unknown, schema: SchemaConfig): PageKind {\n  if (typeof rawKind === \"string\" && (PAGE_KINDS as readonly string[]).includes(rawKind)) {\n    return rawKind as PageKind;\n  }\n  return schema.defaultKind;\n}\n\n/**\n * Count the [[wikilinks]] in a page body.\n * Pure function so the linter can apply per-kind minimums without re-parsing.\n * @param body - Markdown body text.\n * @returns Number of wikilink references found.\n */\nexport function countWikilinks(body: string): number {\n  const matches = body.match(WIKILINK_PATTERN);\n  return matches ? matches.length : 0;\n}\n\n/**\n * Serialise a schema config to YAML for `llmwiki schema init` to write to disk.\n * The `loadedFrom` field is omitted because it's a runtime-only annotation.\n * @param schema - Resolved schema config.\n * @returns YAML string suitable for writing to a schema file.\n */\nexport function serializeSchemaToYaml(schema: SchemaConfig): string {\n  const serializable = {\n    version: schema.version,\n    defaultKind: schema.defaultKind,\n    kinds: schema.kinds,\n    seedPages: schema.seedPages,\n  };\n  return yaml.dump(serializable, { lineWidth: -1, quotingType: '\"' });\n}\n","/**\n * Semantic dependency tracking for cross-source concept sharing.\n *\n * When multiple source files contribute to the same concept, a change in one\n * source should trigger recompilation of that concept using content from ALL\n * contributing sources. This module builds a reverse index from concepts back\n * to their source files, then identifies which unchanged sources are affected\n * by changes to other sources that share concepts with them.\n *\n * Without this, if sources A and B both produce concept X and source A changes,\n * concept X would be regenerated using only source A's content — losing source\n * B's contribution entirely.\n */\n\nimport { readState, updateSourceState, writeState } from \"../utils/state.js\";\nimport { slugify } from \"../utils/markdown.js\";\nimport * as output from \"../utils/output.js\";\nimport type { WikiState, SourceChange, ExtractedConcept } from \"../utils/types.js\";\n\nexport interface ExtractionResult {\n  sourceFile: string;\n  sourcePath: string;\n  sourceContent: string;\n  concepts: ExtractedConcept[];\n}\n\n/**\n * Build a reverse map from concept slugs to the source files that produced them.\n * @param sources - The sources record from WikiState.\n * @returns Map where keys are concept slugs and values are arrays of source filenames.\n */\nfunction buildConceptToSourcesMap(\n  sources: WikiState[\"sources\"],\n): Map<string, string[]> {\n  const conceptMap = new Map<string, string[]>();\n\n  for (const [sourceFile, entry] of Object.entries(sources)) {\n    for (const slug of entry.concepts) {\n      const existing = conceptMap.get(slug);\n      if (existing) {\n        existing.push(sourceFile);\n      } else {\n        conceptMap.set(slug, [sourceFile]);\n      }\n    }\n  }\n\n  return conceptMap;\n}\n\n/** Extract filenames from changes matching a given status. */\nfunction filesByStatus(\n  changes: SourceChange[],\n  ...statuses: SourceChange[\"status\"][]\n): Set<string> {\n  const statusSet = new Set(statuses);\n  return new Set(\n    changes.filter((c) => statusSet.has(c.status)).map((c) => c.file),\n  );\n}\n\n/**\n * Collect co-contributors for a source's concepts, skipping files in the\n * exclusion sets. Mutates `out` by adding newly discovered contributors.\n */\nfunction collectSharedContributors(\n  sourceFile: string,\n  state: WikiState,\n  conceptMap: Map<string, string[]>,\n  excludeSets: Set<string>[],\n  out: Set<string>,\n): void {\n  const sourceEntry = state.sources[sourceFile];\n  if (!sourceEntry) return;\n\n  for (const slug of sourceEntry.concepts) {\n    const contributors = conceptMap.get(slug);\n    if (!contributors || contributors.length < 2) continue;\n\n    for (const contributor of contributors) {\n      const isExcluded = excludeSets.some((s) => s.has(contributor));\n      if (!isExcluded) out.add(contributor);\n    }\n  }\n}\n\n/**\n * Identify unchanged sources that need recompilation because they share\n * concepts with directly changed sources. This enables correct cross-source\n * concept regeneration — ensuring shared concepts are rebuilt with content\n * from ALL contributing sources.\n *\n * Deleted sources are intentionally excluded: recompiling a concept-mate of\n * a deleted source would regenerate the page from fewer sources, losing\n * content. Shared concepts from deleted sources are preserved as-is by\n * markOrphaned (which skips shared concepts).\n *\n * @param state - The current persisted WikiState.\n * @param directChanges - Changes detected by hash comparison.\n * @returns Filenames of indirectly affected sources not already in the changed list.\n */\nexport function findAffectedSources(\n  state: WikiState,\n  directChanges: SourceChange[],\n): string[] {\n  const changedFiles = filesByStatus(directChanges, \"new\", \"changed\");\n  const deletedFiles = filesByStatus(directChanges, \"deleted\");\n  const conceptMap = buildConceptToSourcesMap(state.sources);\n  const affected = new Set<string>();\n\n  for (const changedFile of changedFiles) {\n    collectSharedContributors(\n      changedFile, state, conceptMap,\n      [changedFiles, deletedFiles, affected],\n      affected,\n    );\n  }\n\n  return Array.from(affected);\n}\n\n/**\n * Find concept slugs that must NOT be regenerated during this compile batch.\n * A slug is \"frozen\" when it was shared between a deleted source and at least\n * one surviving source. Regenerating it would overwrite the existing page\n * (which has combined content from all prior contributors) with content from\n * only the surviving sources, silently losing the deleted source's contribution.\n * @param state - Current persisted state.\n * @param changes - All detected source changes in this batch.\n * @returns Set of concept slugs that compileSource should skip.\n */\nexport function findFrozenSlugs(\n  state: WikiState,\n  changes: SourceChange[],\n): Set<string> {\n  // Start with persisted frozen slugs from prior batches.\n  const frozen = new Set<string>(state.frozenSlugs ?? []);\n\n  // Add new frozen slugs from deletions in this batch.\n  const deletedFiles = changes\n    .filter((c) => c.status === \"deleted\")\n    .map((c) => c.file);\n\n  const conceptMap = buildConceptToSourcesMap(state.sources);\n\n  for (const file of deletedFiles) {\n    const entry = state.sources[file];\n    if (!entry) continue;\n\n    for (const slug of entry.concepts) {\n      const contributors = conceptMap.get(slug);\n      if (contributors && contributors.length > 1) {\n        frozen.add(slug);\n      }\n    }\n  }\n\n  return frozen;\n}\n\n/**\n * Unfreeze slugs that were successfully regenerated by all their current\n * contributors, then persist the remaining frozen set to state.\n * A slug is safe to unfreeze when every source that claims it in state\n * was compiled in this batch and successfully extracted it.\n */\nexport async function persistFrozenSlugs(\n  root: string,\n  frozenSlugs: Set<string>,\n  successfulExtractions: ExtractionResult[],\n): Promise<void> {\n  const currentState = await readState(root);\n  const conceptMap = buildConceptToSourcesMap(currentState.sources);\n\n  // Concepts successfully extracted in this batch, keyed by slug.\n  const extractedBy = new Set<string>();\n  for (const result of successfulExtractions) {\n    if (result.concepts.length === 0) continue;\n    for (const c of result.concepts) {\n      extractedBy.add(slugify(c.concept));\n    }\n  }\n  const compiledFiles = new Set(\n    successfulExtractions\n      .filter((r) => r.concepts.length > 0)\n      .map((r) => r.sourceFile),\n  );\n\n  const remaining = new Set<string>();\n  for (const slug of frozenSlugs) {\n    const owners = conceptMap.get(slug) ?? [];\n    // Unfreeze only if ALL current owners were compiled and extracted it.\n    const allOwnersCompiled = owners.length > 0\n      && owners.every((f) => compiledFiles.has(f))\n      && extractedBy.has(slug);\n\n    if (!allOwnersCompiled) remaining.add(slug);\n  }\n\n  const stateToSave = { ...currentState, frozenSlugs: Array.from(remaining) };\n  await writeState(root, stateToSave);\n}\n\n/**\n * Collect concept slugs from extractions that were not in the source's\n * previous concept list — these are \"newly gained\" concepts that\n * findAffectedSources could not have matched pre-extraction.\n */\nfunction collectFreshSlugs(\n  extractions: ExtractionResult[],\n  state: WikiState,\n): Set<string> {\n  const freshSlugs = new Set<string>();\n\n  for (const result of extractions) {\n    const oldConcepts = new Set(state.sources[result.sourceFile]?.concepts ?? []);\n    for (const c of result.concepts) {\n      const slug = slugify(c.concept);\n      if (!oldConcepts.has(slug)) freshSlugs.add(slug);\n    }\n  }\n\n  return freshSlugs;\n}\n\n/**\n * Find unchanged sources that own any of the given slugs, excluding files\n * present in the provided exclusion sets.\n */\nfunction findSlugOwners(\n  slugs: Set<string>,\n  conceptMap: Map<string, string[]>,\n  excludeSets: Set<string>[],\n): string[] {\n  const affected = new Set<string>();\n\n  for (const slug of slugs) {\n    const owners = conceptMap.get(slug);\n    if (!owners) continue;\n    for (const owner of owners) {\n      const isExcluded = excludeSets.some((s) => s.has(owner));\n      if (!isExcluded) affected.add(owner);\n    }\n  }\n\n  return Array.from(affected);\n}\n\n/**\n * Post-extraction check for compiled sources whose freshly extracted concepts\n * overlap with unchanged sources not already in the batch. Covers two cases\n * that findAffectedSources (pre-extraction) cannot detect:\n *   1. New sources have no state entry, so their concepts are unknown.\n *   2. Changed sources may gain concepts they didn't previously have.\n * @param extractions - Results from Phase 1 extraction.\n * @param state - Current persisted state.\n * @param allChanges - Full changes array including deleted/unchanged entries.\n * @returns Filenames of unchanged sources that share concepts with compiled sources.\n */\nexport function findLateAffectedSources(\n  extractions: ExtractionResult[],\n  state: WikiState,\n  allChanges: SourceChange[],\n): string[] {\n  const compilingFiles = filesByStatus(allChanges, \"new\", \"changed\");\n  const deletedFiles = filesByStatus(allChanges, \"deleted\");\n  const conceptMap = buildConceptToSourcesMap(state.sources);\n  const freshSlugs = collectFreshSlugs(extractions, state);\n\n  return findSlugOwners(freshSlugs, conceptMap, [compilingFiles, deletedFiles]);\n}\n\n/**\n * Find concept slugs from a source that are also produced by other sources.\n * Used by markOrphaned to skip orphaning shared concepts when a source is\n * deleted — preserving combined content from prior compilations.\n * @param sourceFile - The source being checked.\n * @param state - Current persisted state.\n * @returns Set of slugs that have at least one other contributing source.\n */\nexport function findSharedConcepts(\n  sourceFile: string,\n  state: WikiState,\n): Set<string> {\n  const shared = new Set<string>();\n  const sourceEntry = state.sources[sourceFile];\n  if (!sourceEntry) return shared;\n\n  const conceptMap = buildConceptToSourcesMap(state.sources);\n\n  for (const slug of sourceEntry.concepts) {\n    const contributors = conceptMap.get(slug);\n    if (contributors && contributors.length > 1) {\n      shared.add(slug);\n    }\n  }\n\n  return shared;\n}\n\n/**\n * Freeze concepts from failed extractions and persist their state with a\n * blank hash so they retry on the next compile. Preserves old concept lists\n * to keep dependency tracking intact.\n */\nexport async function freezeFailedExtractions(\n  root: string,\n  results: ExtractionResult[],\n  frozenSlugs: Set<string>,\n): Promise<void> {\n  for (const result of results) {\n    if (result.concepts.length > 0) continue;\n\n    output.status(\"!\", output.warn(`${result.sourceFile}: no concepts — will retry.`));\n    const currentState = await readState(root);\n    const oldConcepts = currentState.sources[result.sourceFile]?.concepts ?? [];\n    for (const slug of oldConcepts) frozenSlugs.add(slug);\n\n    await updateSourceState(root, result.sourceFile, {\n      hash: \"\",\n      concepts: oldConcepts,\n      compiledAt: new Date().toISOString(),\n    });\n  }\n}\n","/**\n * Orphan management for deleted source files.\n *\n * When a source is deleted, its exclusively-owned concept pages are marked\n * orphaned (orphaned: true in frontmatter). Shared concepts are preserved\n * to avoid losing combined content from prior compilations.\n *\n * After compilation, frozen slugs (shared concepts that lost a contributor)\n * are checked against the updated state. Any that lost ALL owners are\n * orphaned as a cleanup pass.\n */\n\nimport path from \"path\";\nimport { readState, removeSourceState } from \"../utils/state.js\";\nimport {\n  atomicWrite,\n  safeReadFile,\n  parseFrontmatter,\n} from \"../utils/markdown.js\";\nimport { findSharedConcepts } from \"./deps.js\";\nimport * as output from \"../utils/output.js\";\nimport { CONCEPTS_DIR } from \"../utils/constants.js\";\n\n/**\n * Mark wiki pages as orphaned when their source is deleted.\n * Only orphans concepts exclusively owned by the deleted source.\n * Shared concepts (contributed to by other live sources) are preserved\n * as-is to avoid losing combined content from prior compilations.\n */\nexport async function markOrphaned(\n  root: string,\n  sourceFile: string,\n  state: Awaited<ReturnType<typeof readState>>,\n): Promise<void> {\n  const sourceEntry = state.sources[sourceFile];\n  if (!sourceEntry) return;\n\n  const sharedSlugs = findSharedConcepts(sourceFile, state);\n\n  for (const slug of sourceEntry.concepts) {\n    if (sharedSlugs.has(slug)) {\n      output.status(\"i\", output.dim(`Kept: ${slug}.md (shared with other sources)`));\n      continue;\n    }\n\n    await orphanPage(root, slug, \"source deleted\");\n  }\n\n  await removeSourceState(root, sourceFile);\n}\n\n/**\n * Check frozen slugs against the updated state after compilation.\n * If no source still claims a frozen slug, orphan its page so it doesn't\n * linger as an untracked stale file.\n */\nexport async function orphanUnownedFrozenPages(\n  root: string,\n  frozenSlugs: Set<string>,\n): Promise<void> {\n  const currentState = await readState(root);\n  const ownedSlugs = new Set<string>();\n  for (const entry of Object.values(currentState.sources)) {\n    for (const slug of entry.concepts) ownedSlugs.add(slug);\n  }\n\n  for (const slug of frozenSlugs) {\n    if (ownedSlugs.has(slug)) continue;\n    await orphanPage(root, slug, \"no remaining sources\");\n  }\n}\n\n/**\n * Mark a single concept page as orphaned if it exists and isn't already marked.\n * @param root - Project root directory.\n * @param slug - Concept slug to orphan.\n * @param reason - Human-readable reason for the log message.\n */\nasync function orphanPage(root: string, slug: string, reason: string): Promise<void> {\n  const pagePath = path.join(root, CONCEPTS_DIR, `${slug}.md`);\n  const content = await safeReadFile(pagePath);\n  if (!content) return;\n\n  const { meta } = parseFrontmatter(content);\n  if (meta.orphaned === true) return;\n\n  const updated = content.replace(\"---\\n\", \"---\\norphaned: true\\n\");\n  await atomicWrite(pagePath, updated);\n  output.status(\"⚠\", output.warn(`Orphaned: ${slug}.md (${reason})`));\n}\n","/**\n * Interlink resolution for wiki pages.\n *\n * Rule-based (not LLM-based) pass that scans wiki pages for concept title\n * mentions and wraps them in [[slug|Title]] wikilinks. The piped alias form\n * keeps Obsidian link resolution stable when a page's filename (slug) differs\n * from its display title.\n *\n * Complexity: O(changed * total) per incremental compile.\n * Full recompile degrades to O(total^2).\n */\n\nimport { readdir, readFile } from \"fs/promises\";\nimport path from \"path\";\nimport { existsSync } from \"fs\";\nimport { atomicWrite, parseFrontmatter } from \"../utils/markdown.js\";\nimport { CONCEPTS_DIR } from \"../utils/constants.js\";\nimport * as output from \"../utils/output.js\";\n\ninterface PageInfo {\n  slug: string;\n  title: string;\n  filePath: string;\n}\n\n/** Build an index of all wiki page titles from the concepts directory. */\nasync function buildTitleIndex(root: string): Promise<PageInfo[]> {\n  const conceptsDir = path.join(root, CONCEPTS_DIR);\n  if (!existsSync(conceptsDir)) return [];\n\n  const files = await readdir(conceptsDir);\n  const pages: PageInfo[] = [];\n\n  for (const file of files) {\n    if (!file.endsWith(\".md\")) continue;\n\n    const filePath = path.join(conceptsDir, file);\n    const content = await readFile(filePath, \"utf-8\");\n    const { meta } = parseFrontmatter(content);\n\n    if (meta.title && typeof meta.title === \"string\" && !meta.orphaned) {\n      pages.push({\n        slug: file.replace(/\\.md$/, \"\"),\n        title: meta.title,\n        filePath,\n      });\n    }\n  }\n\n  return pages;\n}\n\n/** Check if a position is inside an existing [[wikilink]]. */\nfunction isInsideWikilink(text: string, position: number): boolean {\n  const before = text.lastIndexOf(\"[[\", position);\n  const after = text.indexOf(\"]]\", position);\n  if (before === -1 || after === -1) return false;\n\n  const closeBefore = text.indexOf(\"]]\", before);\n  return closeBefore >= position;\n}\n\n/** Check if a position is inside a ^[...] citation marker. */\nfunction isInsideCitation(text: string, position: number): boolean {\n  const before = text.lastIndexOf(\"^[\", position);\n  const after = text.indexOf(\"]\", position);\n  if (before === -1 || after === -1) return false;\n\n  const closeBefore = text.indexOf(\"]\", before);\n  return closeBefore >= position;\n}\n\n/** Check if a match is at a word boundary. */\nfunction isWordBoundary(text: string, start: number, end: number): boolean {\n  const before = start === 0 || /[\\s,.:;!?()\\[\\]{}/\"']/.test(text[start - 1]);\n  const after = end >= text.length || /[\\s,.:;!?()\\[\\]{}/\"']/.test(text[end]);\n  return before && after;\n}\n\n/** Find all regex matches for a title in the text, returned as position spans. */\nfunction findTitleMatches(text: string, title: string): { start: number; end: number }[] {\n  const escaped = title.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n  const regex = new RegExp(escaped, \"gi\");\n  const matches: { start: number; end: number }[] = [];\n  let match;\n\n  while ((match = regex.exec(text)) !== null) {\n    matches.push({ start: match.index, end: match.index + match[0].length });\n  }\n\n  return matches;\n}\n\n/** Determine whether a match position is eligible for wikilink insertion. */\nfunction isLinkablePosition(text: string, start: number, end: number): boolean {\n  if (isInsideWikilink(text, start)) return false;\n  if (isInsideCitation(text, start)) return false;\n  return isWordBoundary(text, start, end);\n}\n\n/**\n * Add [[wikilinks]] to a page's body for any title mentions.\n * Skips already-linked text and non-word-boundary matches.\n */\nfunction addWikilinks(body: string, titles: PageInfo[], selfTitle: string): string {\n  let result = body;\n  const selfLower = selfTitle.toLowerCase();\n\n  for (const page of titles) {\n    if (page.title.toLowerCase() === selfLower) continue;\n\n    const matches = findTitleMatches(result, page.title);\n\n    // Process matches in reverse to preserve positions\n    for (const m of matches.reverse()) {\n      if (!isLinkablePosition(result, m.start, m.end)) continue;\n      result = result.slice(0, m.start) + `[[${page.slug}|${page.title}]]` + result.slice(m.end);\n    }\n  }\n\n  return result;\n}\n\n/**\n * Run interlink resolution on changed and affected pages.\n *\n * Two passes:\n * 1. Outbound: changed pages get [[wikilinks]] for any title they mention.\n * 2. Inbound: ALL pages get scanned for mentions of newly created titles.\n *    This ensures existing pages link to new concepts without a full recompile.\n *\n * Complexity: O(changed * total) for outbound, O(newTitles * total) for inbound.\n */\nexport async function resolveLinks(\n  root: string,\n  changedSlugs: string[],\n  newSlugs: string[],\n): Promise<number> {\n  const titleIndex = await buildTitleIndex(root);\n  if (titleIndex.length === 0) return 0;\n\n  let linkCount = 0;\n\n  // Pass 1: outbound links on changed pages\n  linkCount += await resolveOutboundLinks(titleIndex, changedSlugs);\n\n  // Pass 2: inbound links on all pages for new titles\n  linkCount += await resolveInboundLinks(titleIndex, newSlugs);\n\n  if (linkCount > 0) {\n    output.status(\"🔗\", output.dim(`Resolved links in ${linkCount} page(s)`));\n  }\n\n  return linkCount;\n}\n\n/** Add outbound [[wikilinks]] to changed pages for any title they mention. */\nasync function resolveOutboundLinks(\n  titleIndex: PageInfo[],\n  changedSlugs: string[],\n): Promise<number> {\n  let count = 0;\n\n  for (const page of titleIndex) {\n    if (!changedSlugs.includes(page.slug)) continue;\n    const didLink = await linkPage(page, titleIndex);\n    if (didLink) count++;\n  }\n\n  return count;\n}\n\n/** Scan ALL pages for mentions of newly created concept titles. */\nasync function resolveInboundLinks(\n  titleIndex: PageInfo[],\n  newSlugs: string[],\n): Promise<number> {\n  if (newSlugs.length === 0) return 0;\n\n  const newTitles = titleIndex.filter((p) => newSlugs.includes(p.slug));\n  if (newTitles.length === 0) return 0;\n\n  let count = 0;\n\n  for (const page of titleIndex) {\n    // Skip pages that were already processed in outbound pass\n    if (newSlugs.includes(page.slug)) continue;\n\n    const content = await readFile(page.filePath, \"utf-8\");\n    const { body } = parseFrontmatter(content);\n    const linked = addWikilinks(body, newTitles, page.title);\n\n    if (linked !== body) {\n      const newContent = content.replace(body, linked);\n      await atomicWrite(page.filePath, newContent);\n      count++;\n    }\n  }\n\n  return count;\n}\n\n/** Add wikilinks to a single page, writing atomically if changed. */\nasync function linkPage(page: PageInfo, titleIndex: PageInfo[]): Promise<boolean> {\n  const content = await readFile(page.filePath, \"utf-8\");\n  const { body } = parseFrontmatter(content);\n  const linked = addWikilinks(body, titleIndex, page.title);\n\n  if (linked === body) return false;\n\n  const newContent = content.replace(body, linked);\n  await atomicWrite(page.filePath, newContent);\n  return true;\n}\n","/**\n * Wiki index generator.\n *\n * Scans all concept pages in wiki/concepts/, extracts frontmatter metadata,\n * and produces wiki/index.md with a sorted list of all concepts and their\n * summaries. Used after each compilation pass.\n */\n\nimport { readdir } from \"fs/promises\";\nimport path from \"path\";\nimport { atomicWrite, safeReadFile, parseFrontmatter } from \"../utils/markdown.js\";\nimport { CONCEPTS_DIR, QUERIES_DIR, INDEX_FILE } from \"../utils/constants.js\";\nimport * as output from \"../utils/output.js\";\nimport type { PageSummary } from \"../utils/types.js\";\n\n/**\n * Generate the wiki/index.md listing all concept pages with summaries.\n * @param root - Project root directory.\n */\nexport async function generateIndex(root: string): Promise<void> {\n  output.status(\"*\", output.info(\"Generating index...\"));\n\n  const conceptsPath = path.join(root, CONCEPTS_DIR);\n  const queriesPath = path.join(root, QUERIES_DIR);\n  const concepts = await collectPageSummaries(conceptsPath);\n  const queries = await collectPageSummaries(queriesPath);\n\n  concepts.sort((a, b) => a.title.localeCompare(b.title));\n  queries.sort((a, b) => a.title.localeCompare(b.title));\n\n  const indexContent = buildIndexContent(concepts, queries);\n  const indexPath = path.join(root, INDEX_FILE);\n  await atomicWrite(indexPath, indexContent);\n\n  const total = concepts.length + queries.length;\n  output.status(\"+\", output.success(`Index updated with ${total} pages.`));\n}\n\n/** A scanned page paired with its parsed frontmatter. */\ninterface ScannedPage {\n  slug: string;\n  meta: Record<string, unknown>;\n}\n\n/**\n * Scan a wiki directory and return every .md page paired with its parsed\n * frontmatter. Read-only utility shared by index generation and the MCP\n * server's status tool.\n * @param dirPath - Absolute path to a wiki page directory.\n * @returns Array of {slug, meta} entries — empty when the directory is missing.\n */\nexport async function scanWikiPages(dirPath: string): Promise<ScannedPage[]> {\n  let files: string[];\n  try {\n    files = await readdir(dirPath);\n  } catch {\n    return [];\n  }\n\n  const scanned: ScannedPage[] = [];\n  for (const file of files.filter((f) => f.endsWith(\".md\"))) {\n    const content = await safeReadFile(path.join(dirPath, file));\n    const { meta } = parseFrontmatter(content);\n    scanned.push({ slug: file.replace(/\\.md$/, \"\"), meta });\n  }\n  return scanned;\n}\n\n/**\n * Project a wiki directory into PageSummary entries (excludes orphaned and\n * untitled pages). Built on top of scanWikiPages so the MCP server can share\n * the underlying scan logic without re-reading the directory.\n * @param conceptsPath - Absolute path to wiki/concepts/.\n * @returns Array of page summary objects.\n */\nexport async function collectPageSummaries(\n  conceptsPath: string,\n): Promise<PageSummary[]> {\n  const scanned = await scanWikiPages(conceptsPath);\n  return scanned\n    .filter(({ meta }) => meta.title && typeof meta.title === \"string\" && !meta.orphaned)\n    .map(({ slug, meta }) => ({\n      title: meta.title as string,\n      slug,\n      summary: typeof meta.summary === \"string\" ? meta.summary : \"\",\n    }));\n}\n\n/** Strip [[wikilink]] brackets from text, leaving the inner text intact. */\nfunction stripWikilinks(text: string): string {\n  return text.replace(/\\[\\[([^\\]]+)\\]\\]/g, \"$1\");\n}\n\n/**\n * Build the index.md markdown content from page summaries.\n * @param pages - Sorted array of page summaries.\n * @returns Full index.md content string.\n */\nfunction buildIndexContent(concepts: PageSummary[], queries: PageSummary[]): string {\n  const lines = [\"# Knowledge Wiki\", \"\", \"## Concepts\", \"\"];\n\n  for (const page of concepts) {\n    lines.push(`- **[[${page.slug}|${page.title}]]** — ${stripWikilinks(page.summary)}`);\n  }\n\n  if (queries.length > 0) {\n    lines.push(\"\", \"## Saved Queries\", \"\");\n    for (const page of queries) {\n      lines.push(`- **[[${page.slug}|${page.title}]]** — ${stripWikilinks(page.summary)}`);\n    }\n  }\n\n  const total = concepts.length + queries.length;\n  lines.push(\"\");\n  lines.push(`_${total} pages | Generated ${new Date().toISOString()}_`);\n  lines.push(\"\");\n\n  return lines.join(\"\\n\");\n}\n","/**\n * Per-concept prompt-budget enforcement (issue #39).\n *\n * When the same concept is extracted from many overlapping sources, the\n * page-generation prompt would otherwise concatenate every full source\n * — linear in source count — and reliably blow past the LLM provider's\n * context window. This module clips each contributing source's slice to\n * a fair share of a configurable total budget and emits a single warning\n * when truncation kicks in.\n *\n * The fix is deliberately defensive (proportional truncation) rather than\n * smart (semantic ranking / summarisation). It prevents crashes while a\n * deeper retrieval-driven solution is designed.\n */\n\nimport * as output from \"../utils/output.js\";\nimport {\n  DEFAULT_PROMPT_BUDGET_CHARS,\n  PROMPT_BUDGET_ENV_VAR,\n} from \"../utils/constants.js\";\n\n/** Marker appended to a source slice when it was truncated to fit the budget. */\nconst TRUNCATION_MARKER = \"\\n\\n[…truncated for prompt budget — see #39…]\";\n\n/** A single source's contribution to the combined per-concept content. */\nexport interface SourceSlice {\n  /** Source filename (e.g. \"ml-paper.md\") shown as a section header in the prompt. */\n  file: string;\n  /** Raw extracted source content, before any budgeting. */\n  content: string;\n}\n\n/**\n * Resolve the active prompt-budget character cap. Reads the\n * `LLMWIKI_PROMPT_BUDGET_CHARS` env var when present and parseable; falls\n * back to `DEFAULT_PROMPT_BUDGET_CHARS`. Invalid values (non-numeric or\n * <= 0) are ignored so a typo can't accidentally truncate every prompt\n * to nothing.\n */\nexport function resolvePromptBudgetChars(): number {\n  const raw = process.env[PROMPT_BUDGET_ENV_VAR];\n  if (!raw) return DEFAULT_PROMPT_BUDGET_CHARS;\n  const parsed = Number.parseInt(raw, 10);\n  if (!Number.isFinite(parsed) || parsed <= 0) return DEFAULT_PROMPT_BUDGET_CHARS;\n  return parsed;\n}\n\n/**\n * Combine per-source slices into the single content blob the LLM prompt\n * receives, applying a fair-share budget when the raw total would exceed\n * the configured ceiling. When no truncation is needed the output is\n * byte-identical to the previous unbudgeted concatenation, so existing\n * compile output is unchanged for typical workloads.\n *\n * @param concept - Human-readable concept title (used in the warning only).\n * @param slices - One entry per contributing source, in arrival order.\n * @returns The combined content string suitable for buildPagePrompt.\n */\nexport function buildBudgetedCombinedContent(\n  concept: string,\n  slices: SourceSlice[],\n): string {\n  const budget = resolvePromptBudgetChars();\n  const totalRaw = slices.reduce((sum, s) => sum + s.content.length, 0);\n\n  if (totalRaw <= budget) {\n    return formatSlices(slices);\n  }\n\n  const perSource = Math.max(1, Math.floor(budget / slices.length));\n  warnTruncation(concept, totalRaw, slices.length, perSource, budget);\n\n  const trimmed = slices.map((s) =>\n    s.content.length > perSource\n      ? { ...s, content: s.content.slice(0, perSource) + TRUNCATION_MARKER }\n      : s,\n  );\n  return formatSlices(trimmed);\n}\n\n/**\n * Prepend right-aligned 1-indexed line numbers to each line of source content.\n * Gives the LLM explicit anchors so its ^[file.md:N-M] citations are accurate.\n */\nfunction numberLines(content: string): string {\n  const lines = content.split(\"\\n\");\n  const width = String(lines.length).length;\n  return lines\n    .map((line, i) => `${String(i + 1).padStart(width)} | ${line}`)\n    .join(\"\\n\");\n}\n\n/**\n * Clip a single source's content to the active prompt budget and prepend line\n * numbers, so a prompt that asks the model for line spans actually shows the\n * model numbered lines (and never exceeds the budget). Used by the rule\n * extractor, which feeds one source per call rather than a merged concept.\n *\n * @param file - Source filename, for the truncation warning only.\n * @param content - Raw source content.\n * @returns Numbered (and, when over budget, truncated) content.\n */\nexport function budgetAndNumberSource(file: string, content: string): string {\n  const budget = resolvePromptBudgetChars();\n  if (content.length <= budget) {\n    return numberLines(content);\n  }\n  warnTruncation(file, content.length, 1, budget, budget);\n  return numberLines(content.slice(0, budget) + TRUNCATION_MARKER);\n}\n\n/** Render the slice list using the same `--- SOURCE: ---` headers the LLM is taught to read. */\nfunction formatSlices(slices: SourceSlice[]): string {\n  return slices\n    .map((s) => `--- SOURCE: ${s.file} ---\\n\\n${numberLines(s.content)}`)\n    .join(\"\\n\\n\");\n}\n\n/** Emit a single, actionable warning when the budget kicks in for a concept. */\nfunction warnTruncation(\n  concept: string,\n  totalRaw: number,\n  sourceCount: number,\n  perSource: number,\n  budget: number,\n): void {\n  output.status(\n    \"!\",\n    output.warn(\n      `Combined source content for \"${concept}\" (${totalRaw.toLocaleString()} chars across ` +\n        `${sourceCount} sources) exceeds the ${budget.toLocaleString()}-char prompt budget; ` +\n        `truncating each source to ~${perSource.toLocaleString()} chars. ` +\n        `Raise via ${PROMPT_BUDGET_ENV_VAR} when running against larger-context models.`,\n    ),\n  );\n}\n","/**\n * Obsidian integration helpers for the llmwiki knowledge compiler.\n *\n * Provides two capabilities:\n * 1. Enriching wiki page frontmatter with tags and aliases for better\n *    Obsidian graph navigation and search.\n * 2. Generating a Map of Content (MOC) page that groups concept pages\n *    by tag for easy browsing.\n */\n\nimport { readdir } from \"fs/promises\";\nimport path from \"path\";\nimport { slugify, atomicWrite, safeReadFile, parseFrontmatter } from \"../utils/markdown.js\";\nimport { CONCEPTS_DIR, MOC_FILE } from \"../utils/constants.js\";\n\n/** Minimum word count to generate an abbreviation alias. */\nconst ABBREVIATION_MIN_WORDS = 3;\n\n/** Conjunctions that trigger a word-swap alias. */\nconst SWAP_CONJUNCTIONS = [\" and \", \" or \"];\n\n/**\n * Enrich a frontmatter object with Obsidian-specific tags and aliases.\n * Mutates the frontmatter object in place.\n * @param frontmatter - The frontmatter object to enrich.\n * @param conceptTitle - The human-readable concept title.\n * @param tags - Tags from extraction (may be empty).\n */\nexport function addObsidianMeta(\n  frontmatter: Record<string, unknown>,\n  conceptTitle: string,\n  tags: string[],\n): void {\n  frontmatter.tags = tags;\n  frontmatter.aliases = generateAliases(conceptTitle);\n}\n\n/**\n * Generate deterministic aliases from a concept title.\n * Produces up to three alias variants:\n * - Slug form (e.g., \"gradient-descent\")\n * - Word-swap around conjunctions (e.g., \"Optimization and Gradient Descent\")\n * - Abbreviation from first letters for 3+ word titles (e.g., \"RAG\")\n * @param title - The concept title to derive aliases from.\n * @returns Array of aliases that differ from the original title.\n */\nfunction generateAliases(title: string): string[] {\n  const aliases: string[] = [];\n  const slug = slugify(title);\n\n  if (slug !== title) {\n    aliases.push(slug);\n  }\n\n  const swapAlias = generateSwapAlias(title);\n  if (swapAlias) {\n    aliases.push(swapAlias);\n  }\n\n  const abbreviation = generateAbbreviation(title);\n  if (abbreviation) {\n    aliases.push(abbreviation);\n  }\n\n  return aliases;\n}\n\n/**\n * Generate a word-swap alias by reversing parts around a conjunction.\n * E.g., \"Gradient Descent and Optimization\" becomes \"Optimization and Gradient Descent\".\n * @param title - The concept title.\n * @returns The swapped alias, or null if no conjunction found.\n */\nfunction generateSwapAlias(title: string): string | null {\n  for (const conjunction of SWAP_CONJUNCTIONS) {\n    const index = title.toLowerCase().indexOf(conjunction);\n    if (index === -1) continue;\n\n    const before = title.slice(0, index);\n    const after = title.slice(index + conjunction.length);\n    const originalConjunction = title.slice(index, index + conjunction.length);\n    return `${after}${originalConjunction}${before}`;\n  }\n  return null;\n}\n\n/**\n * Generate an abbreviation from first letters of each word for titles with 3+ words.\n * E.g., \"Retrieval Augmented Generation\" becomes \"RAG\".\n * @param title - The concept title.\n * @returns The abbreviation, or null if title has fewer than 3 words.\n */\nfunction generateAbbreviation(title: string): string | null {\n  const words = title.split(/\\s+/);\n  if (words.length < ABBREVIATION_MIN_WORDS) return null;\n\n  const abbreviation = words.map((w) => w[0].toUpperCase()).join(\"\");\n  if (abbreviation === title) return null;\n\n  return abbreviation;\n}\n\n/**\n * Generate a Map of Content (MOC) page grouping concept pages by tag.\n * Reads all concept pages, extracts their tags from frontmatter, and writes\n * a structured MOC.md with sections per tag and an Uncategorized section.\n * @param root - Project root directory.\n */\nexport async function generateMOC(root: string): Promise<void> {\n  const conceptsPath = path.join(root, CONCEPTS_DIR);\n  const pages = await loadConceptPages(conceptsPath);\n\n  const tagGroups = groupPagesByTag(pages);\n  const content = buildMOCContent(tagGroups);\n\n  await atomicWrite(path.join(root, MOC_FILE), content);\n}\n\n/** Minimal page info needed for MOC generation. */\ninterface PageInfo {\n  slug: string;\n  title: string;\n  tags: string[];\n}\n\n/**\n * Load all concept pages and extract their title and tags.\n * @param conceptsPath - Absolute path to the concepts directory.\n * @returns Array of page info objects.\n */\nasync function loadConceptPages(conceptsPath: string): Promise<PageInfo[]> {\n  let files: string[];\n  try {\n    files = await readdir(conceptsPath);\n  } catch {\n    return [];\n  }\n\n  const pages: PageInfo[] = [];\n  for (const file of files) {\n    if (!file.endsWith(\".md\")) continue;\n\n    const content = await safeReadFile(path.join(conceptsPath, file));\n    if (!content) continue;\n\n    const { meta } = parseFrontmatter(content);\n    if (meta.orphaned) continue;\n\n    const slug = file.replace(/\\.md$/, \"\");\n    const title = typeof meta.title === \"string\" ? meta.title : slug;\n    const tags = Array.isArray(meta.tags) ? (meta.tags as string[]) : [];\n    pages.push({ slug, title, tags });\n  }\n\n  return pages;\n}\n\n/**\n * Group pages by their tags into a map. Pages with no tags go under \"Uncategorized\".\n * @param pages - Array of page info objects.\n * @returns Map of tag name to array of page titles.\n */\nfunction groupPagesByTag(pages: PageInfo[]): Map<string, PageInfo[]> {\n  const groups = new Map<string, PageInfo[]>();\n\n  for (const page of pages) {\n    if (page.tags.length === 0) {\n      appendToGroup(groups, \"Uncategorized\", page);\n      continue;\n    }\n\n    for (const tag of page.tags) {\n      appendToGroup(groups, tag, page);\n    }\n  }\n\n  return groups;\n}\n\n/** Append a page to a group, creating the group if needed. */\nfunction appendToGroup(groups: Map<string, PageInfo[]>, key: string, page: PageInfo): void {\n  const existing = groups.get(key);\n  if (existing) {\n    existing.push(page);\n  } else {\n    groups.set(key, [page]);\n  }\n}\n\n/**\n * Build the MOC markdown content from grouped pages.\n * @param tagGroups - Map of tag name to array of page titles.\n * @returns Complete MOC markdown string.\n */\nfunction buildMOCContent(tagGroups: Map<string, PageInfo[]>): string {\n  const lines: string[] = [\"# Map of Content\", \"\"];\n\n  const sortedTags = [...tagGroups.keys()].sort((a, b) => {\n    // \"Uncategorized\" always goes last\n    if (a === \"Uncategorized\") return 1;\n    if (b === \"Uncategorized\") return -1;\n    return a.localeCompare(b);\n  });\n\n  for (const tag of sortedTags) {\n    const pages = tagGroups.get(tag) ?? [];\n    lines.push(`## ${tag}`, \"\");\n    for (const page of pages.sort((a, b) => a.title.localeCompare(b.title))) {\n      lines.push(`- [[${page.slug}|${page.title}]]`);\n    }\n    lines.push(\"\");\n  }\n\n  return lines.join(\"\\n\");\n}\n","/**\n * Helpers for surfacing provenance metadata during compilation.\n *\n * Keeps the compile orchestrator small by isolating the logic that copies\n * confidence/contradiction signals from extracted concepts onto wiki page\n * frontmatter and emits compile-time warnings when contradictions are\n * reported.\n */\n\nimport * as output from \"../utils/output.js\";\nimport { resolveActiveModelId } from \"../utils/provider.js\";\nimport { PROMPT_VERSION } from \"./prompts.js\";\nimport type { ExtractedConcept } from \"../utils/types.js\";\n\n/**\n * Stamp compile-time lineage onto a page's frontmatter: the model id that the\n * active provider would use and the named prompt-contract version. Written when\n * the page is (re)generated, so it records the model/prompt that actually\n * produced the page's current content — unlike an export-time env read, which\n * can attribute a page to a model that never touched it. Surfaced per-page in\n * the JSON export (`ExportPage.modelId` / `promptVersion`).\n * @param fields - Mutable frontmatter record being assembled for a page.\n */\nexport function addModelProvenanceMeta(fields: Record<string, unknown>): void {\n  fields.modelId = resolveActiveModelId();\n  fields.promptVersion = PROMPT_VERSION;\n}\n\n/**\n * Copy provenance metadata fields from an extracted concept onto the\n * frontmatter record, omitting fields the LLM did not provide so existing\n * pages without these fields stay clean.\n * @param fields - Mutable frontmatter record being assembled for a page.\n * @param concept - Source concept whose provenance metadata to apply.\n */\nexport function addProvenanceMeta(\n  fields: Record<string, unknown>,\n  concept: ExtractedConcept,\n): void {\n  if (typeof concept.confidence === \"number\") {\n    fields.confidence = concept.confidence;\n  }\n  if (concept.provenanceState) {\n    fields.provenanceState = concept.provenanceState;\n  }\n  if (concept.contradictedBy && concept.contradictedBy.length > 0) {\n    fields.contradictedBy = concept.contradictedBy;\n  }\n}\n\n/**\n * Print a compile-time warning when a concept reports contradictions with\n * other pages. Returns silently when there is nothing to report.\n * @param conceptTitle - Human-readable title of the concept being compiled.\n * @param concept - The extracted concept whose contradictions to surface.\n */\nexport function reportContradictionWarnings(\n  conceptTitle: string,\n  concept: ExtractedConcept,\n): void {\n  const refs = concept.contradictedBy;\n  if (!refs || refs.length === 0) return;\n  const slugs = refs.map((r) => r.slug).join(\", \");\n  output.status(\n    \"!\",\n    output.warn(`Contradiction reported on \"${conceptTitle}\" — conflicts with: ${slugs}`),\n  );\n}\n","/**\n * Embedding-based semantic search utilities.\n *\n * Maintains a persistent store of page and chunk embeddings in\n * .llmwiki/embeddings.json and provides cosine-similarity retrieval so the\n * query command can narrow hundreds of pages down to a small top-K before\n * calling the selection LLM.\n *\n * The store is additive: successful embedding calls update entries; failures\n * degrade gracefully (caller falls back to full-index selection).\n *\n * The store has two on-disk versions:\n *   - v1: page-level entries only (legacy; still readable).\n *   - v2: page-level entries plus optional chunk-level entries that enable\n *     paragraph-precision retrieval, content-hash-aware incremental updates,\n *     and reranking before final page selection.\n */\n\nimport { readFile, readdir } from \"fs/promises\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport { getProvider, getActiveProviderName } from \"./provider.js\";\nimport { atomicWrite, safeReadFile, parseFrontmatter } from \"./markdown.js\";\nimport {\n  CONCEPTS_DIR,\n  QUERIES_DIR,\n  EMBEDDINGS_FILE,\n  EMBEDDING_TOP_K,\n  EMBEDDING_MODELS,\n} from \"./constants.js\";\nimport { hashChunkText, splitIntoChunks } from \"./retrieval.js\";\nimport * as output from \"./output.js\";\n\n/** Current store version; bumped from 1 → 2 when chunk entries were added. */\nconst STORE_VERSION = 2 as const;\n\n/** A single embedded page record. */\nexport interface EmbeddingEntry {\n  slug: string;\n  title: string;\n  summary: string;\n  vector: number[];\n  updatedAt: string;\n}\n\n/** A single embedded chunk drawn from a page body. */\nexport interface ChunkEmbeddingEntry {\n  slug: string;\n  title: string;\n  chunkIndex: number;\n  contentHash: string;\n  text: string;\n  vector: number[];\n  updatedAt: string;\n}\n\n/** Root shape of .llmwiki/embeddings.json. */\nexport interface EmbeddingStore {\n  version: 1 | 2;\n  model: string;\n  dimensions: number;\n  entries: EmbeddingEntry[];\n  /** Optional in v2 stores; absent in v1 stores. */\n  chunks?: ChunkEmbeddingEntry[];\n}\n\n/** A retrievable page record on disk (concepts/ or queries/). */\ninterface PageRecord {\n  slug: string;\n  title: string;\n  summary: string;\n  body: string;\n}\n\n/**\n * Cosine similarity between two equal-length vectors.\n * Returns 0 when either vector has zero magnitude (safer than NaN for ranking).\n */\nexport function cosineSimilarity(a: number[], b: number[]): number {\n  if (a.length !== b.length || a.length === 0) return 0;\n\n  let dot = 0;\n  let magA = 0;\n  let magB = 0;\n  for (let i = 0; i < a.length; i++) {\n    dot += a[i] * b[i];\n    magA += a[i] * a[i];\n    magB += b[i] * b[i];\n  }\n\n  if (magA === 0 || magB === 0) return 0;\n  return dot / (Math.sqrt(magA) * Math.sqrt(magB));\n}\n\n/** Return the top-K entries most similar to the query vector, sorted descending. */\nexport function findTopK(\n  queryVec: number[],\n  store: EmbeddingStore,\n  k: number,\n): EmbeddingEntry[] {\n  const scored = store.entries.map((entry) => ({\n    entry,\n    score: cosineSimilarity(queryVec, entry.vector),\n  }));\n  scored.sort((left, right) => right.score - left.score);\n  return scored.slice(0, k).map((item) => item.entry);\n}\n\n/** Score and sort chunk entries by cosine similarity, returning the top-K. */\nexport function findTopKChunks(\n  queryVec: number[],\n  chunks: ChunkEmbeddingEntry[],\n  k: number,\n): Array<{ chunk: ChunkEmbeddingEntry; score: number }> {\n  const scored = chunks.map((chunk) => ({\n    chunk,\n    score: cosineSimilarity(queryVec, chunk.vector),\n  }));\n  scored.sort((left, right) => right.score - left.score);\n  return scored.slice(0, k);\n}\n\n/** Read .llmwiki/embeddings.json, returning null if it does not exist. */\nexport async function readEmbeddingStore(root: string): Promise<EmbeddingStore | null> {\n  const filePath = path.join(root, EMBEDDINGS_FILE);\n  if (!existsSync(filePath)) return null;\n  const raw = await readFile(filePath, \"utf-8\");\n  return JSON.parse(raw) as EmbeddingStore;\n}\n\n/** Atomically persist the embedding store. */\nexport async function writeEmbeddingStore(root: string, store: EmbeddingStore): Promise<void> {\n  const filePath = path.join(root, EMBEDDINGS_FILE);\n  await atomicWrite(filePath, JSON.stringify(store, null, 2));\n}\n\n/**\n * Embed the question, look up top-K matches, and return lightweight page records.\n * Returns [] when no store exists so callers can transparently fall back.\n */\nexport async function findRelevantPages(\n  root: string,\n  question: string,\n): Promise<Array<{ slug: string; title: string; summary: string }>> {\n  const store = await loadActiveStore(root, (s) => s.entries.length > 0);\n  if (!store) return [];\n\n  const queryVec = await getProvider().embed(question);\n  return findTopK(queryVec, store, EMBEDDING_TOP_K).map((entry) => ({\n    slug: entry.slug,\n    title: entry.title,\n    summary: entry.summary,\n  }));\n}\n\n/**\n * Look up top-K chunks similar to the question. Returns [] when no chunk-level\n * store exists so callers can fall back to page-level retrieval.\n */\nexport async function findRelevantChunks(\n  root: string,\n  question: string,\n  k: number,\n): Promise<Array<{ chunk: ChunkEmbeddingEntry; score: number }>> {\n  const store = await loadActiveStore(root, (s) => Boolean(s.chunks && s.chunks.length > 0));\n  if (!store) return [];\n  const queryVec = await getProvider().embed(question);\n  return findTopKChunks(queryVec, store.chunks ?? [], k);\n}\n\n/**\n * Read the embedding store, returning null when it is missing, empty (per the\n * caller's predicate), or built with a stale model. Centralises the \"is this\n * store usable for semantic lookup right now?\" check.\n */\nasync function loadActiveStore(\n  root: string,\n  hasContent: (store: EmbeddingStore) => boolean,\n): Promise<EmbeddingStore | null> {\n  const store = await readEmbeddingStore(root);\n  if (!store || !hasContent(store)) return null;\n  const activeModel = resolveEmbeddingModel();\n  if (store.model !== activeModel) {\n    warnStaleEmbeddingStore(store.model, activeModel);\n    return null;\n  }\n  return store;\n}\n\n/** Scan concepts/ and queries/ directories, returning retrievable pages. */\nasync function collectPageRecords(root: string): Promise<PageRecord[]> {\n  const records: PageRecord[] = [];\n  for (const dir of [CONCEPTS_DIR, QUERIES_DIR]) {\n    const absDir = path.join(root, dir);\n    let files: string[];\n    try {\n      files = await readdir(absDir);\n    } catch {\n      continue;\n    }\n    for (const file of files.filter((f) => f.endsWith(\".md\"))) {\n      const record = await readPageRecord(absDir, file);\n      if (record) records.push(record);\n    }\n  }\n  return records;\n}\n\n/** Parse a single page file into a PageRecord, skipping orphans/untitled pages. */\nasync function readPageRecord(absDir: string, file: string): Promise<PageRecord | null> {\n  const content = await safeReadFile(path.join(absDir, file));\n  const { meta, body } = parseFrontmatter(content);\n  if (meta.orphaned || typeof meta.title !== \"string\") return null;\n  return {\n    slug: file.replace(/\\.md$/, \"\"),\n    title: meta.title,\n    summary: typeof meta.summary === \"string\" ? meta.summary : \"\",\n    body,\n  };\n}\n\n/** Build the text that represents a page in the embedding space. */\nfunction buildEmbeddingText(record: PageRecord): string {\n  return record.summary\n    ? `${record.title}\\n\\n${record.summary}`\n    : record.title;\n}\n\n/**\n * Embed every page in `records` whose slug appears in `slugsToEmbed`,\n * returning the new entries. Failures bubble up to the caller.\n */\nasync function embedPages(\n  records: PageRecord[],\n  slugsToEmbed: Set<string>,\n): Promise<EmbeddingEntry[]> {\n  const provider = getProvider();\n  const now = new Date().toISOString();\n  const fresh: EmbeddingEntry[] = [];\n\n  for (const record of records) {\n    if (!slugsToEmbed.has(record.slug)) continue;\n    const vector = await provider.embed(buildEmbeddingText(record));\n    fresh.push({\n      slug: record.slug,\n      title: record.title,\n      summary: record.summary,\n      vector,\n      updatedAt: now,\n    });\n  }\n  return fresh;\n}\n\n/** Tracks which (stored, active) model pairs have already been warned about. */\nconst warnedStaleModels = new Set<string>();\n\n/** Warn once per (stored, active) model pair so queries stay quiet on repeat runs. */\nfunction warnStaleEmbeddingStore(storedModel: string, activeModel: string): void {\n  const key = `${storedModel}→${activeModel}`;\n  if (warnedStaleModels.has(key)) return;\n  warnedStaleModels.add(key);\n  output.status(\n    \"!\",\n    output.warn(\n      `Embedding store was built with \"${storedModel}\" but active embedding model is \"${activeModel}\". ` +\n      `Falling back to full-index selection. Run 'llmwiki compile' to rebuild embeddings.`,\n    ),\n  );\n}\n\n/** Test-only hook: clear the warned-pair cache so each test sees a fresh warning. */\nexport function resetStaleEmbeddingWarnings(): void {\n  warnedStaleModels.clear();\n}\n\n/** Choose the active embedding model name, defaulting to anthropic's voyage model. */\nexport function resolveEmbeddingModel(): string {\n  const providerName = getActiveProviderName();\n  const configuredModel = process.env.LLMWIKI_EMBEDDING_MODEL?.trim();\n  if (configuredModel && (providerName === \"openai\" || providerName === \"ollama\")) {\n    return configuredModel;\n  }\n  return EMBEDDING_MODELS[providerName] ?? EMBEDDING_MODELS.anthropic;\n}\n\n/** Merge fresh embeddings into an existing store, dropping slugs not in liveSlugs. */\nfunction mergeEntries(\n  existing: EmbeddingEntry[],\n  fresh: EmbeddingEntry[],\n  liveSlugs: Set<string>,\n): EmbeddingEntry[] {\n  const bySlug = new Map<string, EmbeddingEntry>();\n  for (const entry of existing) {\n    if (liveSlugs.has(entry.slug)) bySlug.set(entry.slug, entry);\n  }\n  for (const entry of fresh) {\n    bySlug.set(entry.slug, entry);\n  }\n  return Array.from(bySlug.values());\n}\n\n/**\n * Refresh chunk embeddings for the given pages, reusing existing chunk vectors\n * whose contentHash still matches. Pages absent from `records` are pruned.\n */\nasync function refreshChunkEmbeddings(\n  records: PageRecord[],\n  existing: ChunkEmbeddingEntry[],\n  forceAll: boolean,\n): Promise<ChunkEmbeddingEntry[]> {\n  const liveSlugs = new Set(records.map((r) => r.slug));\n  const existingByKey = indexChunksByKey(existing.filter((c) => liveSlugs.has(c.slug)));\n  const now = new Date().toISOString();\n  const fresh: ChunkEmbeddingEntry[] = [];\n\n  for (const record of records) {\n    const pageChunks = await embedRecordChunks(record, existingByKey, forceAll, now);\n    fresh.push(...pageChunks);\n  }\n  return fresh;\n}\n\n/**\n * Embed (or reuse) every chunk for a single page, in order. Reused chunks have\n * their `title` refreshed so a renamed page propagates to the chunk metadata.\n */\nasync function embedRecordChunks(\n  record: PageRecord,\n  existingByKey: Map<string, ChunkEmbeddingEntry>,\n  forceAll: boolean,\n  now: string,\n): Promise<ChunkEmbeddingEntry[]> {\n  const provider = getProvider();\n  const chunkTexts = splitIntoChunks(record.body);\n  const out: ChunkEmbeddingEntry[] = [];\n\n  for (let i = 0; i < chunkTexts.length; i++) {\n    const text = chunkTexts[i];\n    const contentHash = hashChunkText(text);\n    const reused = pickReusableChunk(existingByKey, record.slug, i, contentHash, forceAll);\n    if (reused) {\n      out.push({ ...reused, title: record.title });\n      continue;\n    }\n    const vector = await provider.embed(text);\n    out.push({\n      slug: record.slug, title: record.title, chunkIndex: i,\n      contentHash, text, vector, updatedAt: now,\n    });\n  }\n  return out;\n}\n\n/** Index existing chunks by `${slug}#${chunkIndex}` for O(1) reuse lookup. */\nfunction indexChunksByKey(chunks: ChunkEmbeddingEntry[]): Map<string, ChunkEmbeddingEntry> {\n  const byKey = new Map<string, ChunkEmbeddingEntry>();\n  for (const chunk of chunks) byKey.set(chunkKey(chunk.slug, chunk.chunkIndex), chunk);\n  return byKey;\n}\n\n/** Compose the index key for a chunk lookup. */\nfunction chunkKey(slug: string, chunkIndex: number): string {\n  return `${slug}#${chunkIndex}`;\n}\n\n/** Return the existing chunk vector when its hash still matches and reuse is allowed. */\nfunction pickReusableChunk(\n  byKey: Map<string, ChunkEmbeddingEntry>,\n  slug: string,\n  chunkIndex: number,\n  contentHash: string,\n  forceAll: boolean,\n): ChunkEmbeddingEntry | null {\n  if (forceAll) return null;\n  const existing = byKey.get(chunkKey(slug, chunkIndex));\n  if (!existing) return null;\n  return existing.contentHash === contentHash ? existing : null;\n}\n\n/**\n * Re-embed the given changed slugs and prune any entries whose pages no longer\n * exist on disk. Changed slugs not present as live pages are silently skipped.\n */\nexport async function updateEmbeddings(root: string, changedSlugs: string[]): Promise<void> {\n  const records = await collectPageRecords(root);\n  const liveSlugs = new Set(records.map((r) => r.slug));\n  const embeddingModel = resolveEmbeddingModel();\n  const existingStore = await readEmbeddingStore(root);\n  const modelChanged = Boolean(existingStore && existingStore.model !== embeddingModel);\n  const toEmbed = new Set(changedSlugs.filter((slug) => liveSlugs.has(slug)));\n  const previousEntries = modelChanged ? [] : existingStore?.entries ?? [];\n  const previousChunks = modelChanged ? [] : existingStore?.chunks ?? [];\n\n  // Cold start: embed every page so the store is immediately useful.\n  // Also treat an empty on-disk store as a cold start so that a project\n  // with no ingested pages yet (or a wiped store) gets populated the next\n  // time `compile` runs without needing an explicit slug change.\n  const isEmptyStore = isStoreEmpty(existingStore);\n  if (!existingStore || modelChanged || (isEmptyStore && liveSlugs.size > 0)) {\n    for (const record of records) toEmbed.add(record.slug);\n  }\n\n  if (!shouldRunEmbedding(modelChanged, toEmbed, previousEntries, previousChunks, liveSlugs)) {\n    return;\n  }\n\n  const freshEntries = await embedPages(records, toEmbed);\n  const mergedEntries = mergeEntries(previousEntries, freshEntries, liveSlugs);\n  const mergedChunks = await refreshChunkEmbeddings(records, previousChunks, modelChanged);\n\n  await persistRefreshedStore(root, embeddingModel, mergedEntries, mergedChunks);\n}\n\n/** Persist a freshly merged store and emit a friendly status line. */\nasync function persistRefreshedStore(\n  root: string,\n  embeddingModel: string,\n  entries: EmbeddingEntry[],\n  chunks: ChunkEmbeddingEntry[],\n): Promise<void> {\n  const dimensions = entries[0]?.vector.length ?? chunks[0]?.vector.length ?? 0;\n  const store: EmbeddingStore = {\n    version: STORE_VERSION,\n    model: embeddingModel,\n    dimensions,\n    entries,\n    chunks,\n  };\n  await writeEmbeddingStore(root, store);\n  output.status(\n    \"*\",\n    output.dim(`Embeddings updated (${entries.length} pages, ${chunks.length} chunks).`),\n  );\n}\n\n/** Return true when a store exists on disk but has neither page nor chunk entries. */\nfunction isStoreEmpty(store: EmbeddingStore | null): boolean {\n  if (!store) return false;\n  return store.entries.length === 0 && (!store.chunks || store.chunks.length === 0);\n}\n\n/** Decide whether updateEmbeddings has work to do beyond a no-op. */\nfunction shouldRunEmbedding(\n  modelChanged: boolean,\n  toEmbed: Set<string>,\n  previousEntries: EmbeddingEntry[],\n  previousChunks: ChunkEmbeddingEntry[],\n  liveSlugs: Set<string>,\n): boolean {\n  if (modelChanged) return true;\n  if (toEmbed.size > 0) return true;\n  if (!previousEntries.every((e) => liveSlugs.has(e.slug))) return true;\n  if (!previousChunks.every((c) => liveSlugs.has(c.slug))) return true;\n  // Cold-start case where we have entries but no chunks yet.\n  if (previousEntries.length > 0 && previousChunks.length === 0 && liveSlugs.size > 0) return true;\n  return false;\n}\n","/**\n * Chunked retrieval helpers: text splitting, content hashing, and BM25 reranking.\n *\n * The query pipeline relies on these utilities to:\n *   1. Split a wiki page into paragraph-aligned chunks for embedding.\n *   2. Detect unchanged chunks via a stable content hash so embedding refreshes\n *      can skip work.\n *   3. Rerank a candidate set with a lightweight BM25 score over chunk text,\n *      improving precision over pure cosine similarity for keyword-heavy\n *      questions.\n *\n * No network calls happen here — these are deterministic CPU-side helpers\n * that are easy to unit test and safe to invoke from any code path.\n */\n\nimport { createHash } from \"crypto\";\nimport {\n  CHUNK_MAX_CHARS,\n  CHUNK_MIN_CHARS,\n  CHUNK_TARGET_CHARS,\n} from \"./constants.js\";\n\n/** Stable content hash used to detect chunk-level changes between runs. */\nexport function hashChunkText(text: string): string {\n  return createHash(\"sha256\").update(text, \"utf8\").digest(\"hex\").slice(0, 16);\n}\n\n/**\n * Split a page body into paragraph-aligned chunks bounded by CHUNK_TARGET_CHARS.\n * Trailing fragments smaller than CHUNK_MIN_CHARS are merged into the previous\n * chunk so we never emit a tiny dangling piece. Paragraphs longer than\n * CHUNK_MAX_CHARS are sentence-split before being added.\n *\n * @param body - Raw page body (frontmatter already stripped).\n * @returns Ordered chunk strings; empty array when body has no usable text.\n */\nexport function splitIntoChunks(body: string): string[] {\n  const paragraphs = extractParagraphs(body);\n  if (paragraphs.length === 0) return [];\n\n  const chunks: string[] = [];\n  let buffer = \"\";\n\n  for (const paragraph of paragraphs) {\n    for (const piece of splitOversizedParagraph(paragraph)) {\n      buffer = appendParagraph(buffer, piece, chunks);\n    }\n  }\n\n  if (buffer.length > 0) chunks.push(buffer);\n  return mergeTrailingFragment(chunks);\n}\n\n/** Append a paragraph to the buffer, flushing when the target size is exceeded. */\nfunction appendParagraph(buffer: string, paragraph: string, chunks: string[]): string {\n  const candidate = buffer ? `${buffer}\\n\\n${paragraph}` : paragraph;\n  if (candidate.length <= CHUNK_TARGET_CHARS) return candidate;\n\n  if (buffer.length > 0) {\n    chunks.push(buffer);\n    return paragraph;\n  }\n  // Single paragraph already exceeds target — emit it as a standalone chunk.\n  chunks.push(candidate);\n  return \"\";\n}\n\n/**\n * Merge a too-small trailing chunk back into its predecessor for cleaner\n * ranking. We only merge when the combined size would still respect\n * CHUNK_MAX_CHARS — otherwise the tiny tail stays standalone.\n */\nfunction mergeTrailingFragment(chunks: string[]): string[] {\n  if (chunks.length < 2) return chunks;\n  const last = chunks[chunks.length - 1];\n  if (last.length >= CHUNK_MIN_CHARS) return chunks;\n  const previous = chunks[chunks.length - 2];\n  // +2 covers the \"\\n\\n\" separator length we insert between paragraphs.\n  if (previous.length + last.length + 2 > CHUNK_MAX_CHARS) return chunks;\n  const merged = chunks.slice(0, -2);\n  merged.push(`${previous}\\n\\n${last}`);\n  return merged;\n}\n\n/** Strip whitespace-only paragraphs from a markdown body. */\nfunction extractParagraphs(body: string): string[] {\n  return body\n    .split(/\\n{2,}/)\n    .map((p) => p.trim())\n    .filter((p) => p.length > 0);\n}\n\n/**\n * Sentence-split a paragraph that exceeds CHUNK_MAX_CHARS so the resulting\n * pieces still respect the upper bound. A single sentence longer than the\n * cap is hard-cut at CHUNK_MAX_CHARS — preferable to dropping content.\n */\nfunction splitOversizedParagraph(paragraph: string): string[] {\n  if (paragraph.length <= CHUNK_MAX_CHARS) return [paragraph];\n\n  const sentences = paragraph.split(/(?<=[.!?])\\s+/);\n  const pieces: string[] = [];\n  let buffer = \"\";\n\n  for (const sentence of sentences) {\n    if ((buffer + \" \" + sentence).length > CHUNK_MAX_CHARS && buffer.length > 0) {\n      pieces.push(buffer.trim());\n      buffer = sentence;\n    } else {\n      buffer = buffer ? `${buffer} ${sentence}` : sentence;\n    }\n  }\n\n  if (buffer.length > 0) pieces.push(buffer.trim());\n  return pieces.flatMap(hardCut);\n}\n\n/** Hard-cut a string longer than CHUNK_MAX_CHARS into fixed-size pieces. */\nfunction hardCut(text: string): string[] {\n  if (text.length <= CHUNK_MAX_CHARS) return [text];\n  const pieces: string[] = [];\n  for (let start = 0; start < text.length; start += CHUNK_MAX_CHARS) {\n    pieces.push(text.slice(start, start + CHUNK_MAX_CHARS));\n  }\n  return pieces;\n}\n\n/** A scored candidate that the BM25 reranker accepts. */\ninterface RankableCandidate {\n  text: string;\n  /** Initial similarity score; preserved for debug output and tie-breaking. */\n  baseScore: number;\n}\n\n/** Result of a BM25 rerank: original candidate plus the rerank score. */\ninterface RankedCandidate<T extends RankableCandidate> {\n  candidate: T;\n  score: number;\n}\n\n/**\n * Rerank candidates with BM25 over their `text` field given a free-text query.\n * BM25 is a deterministic keyword-overlap metric that complements semantic\n * similarity well: it boosts chunks that literally mention the query terms.\n *\n * @param query - Natural-language query.\n * @param candidates - Items to rerank; their `baseScore` is used as a tiebreaker.\n * @returns Sorted descending by combined score.\n */\nexport function rerankWithBm25<T extends RankableCandidate>(\n  query: string,\n  candidates: T[],\n): Array<RankedCandidate<T>> {\n  if (candidates.length === 0) return [];\n  const queryTerms = tokenize(query);\n  if (queryTerms.length === 0) {\n    return candidates.map((candidate) => ({ candidate, score: candidate.baseScore }));\n  }\n\n  const docs = candidates.map((c) => tokenize(c.text));\n  const stats = buildCorpusStats(docs);\n  return rankByBm25Score(candidates, docs, queryTerms, stats);\n}\n\n/** Rank candidates by combined BM25 + base semantic score. */\nfunction rankByBm25Score<T extends RankableCandidate>(\n  candidates: T[],\n  docs: string[][],\n  queryTerms: string[],\n  stats: CorpusStats,\n): Array<RankedCandidate<T>> {\n  const scored = candidates.map((candidate, index) => {\n    const lexical = bm25Score(queryTerms, docs[index], stats);\n    return { candidate, score: lexical + candidate.baseScore * BASE_SCORE_WEIGHT };\n  });\n  scored.sort((a, b) => b.score - a.score);\n  return scored;\n}\n\n/** Tokenise a string into lowercase alphanumeric tokens for BM25. */\nfunction tokenize(text: string): string[] {\n  return text.toLowerCase().match(/[a-z0-9]+/g) ?? [];\n}\n\ninterface CorpusStats {\n  /** Document frequency per term: how many docs contain the term. */\n  docFreq: Map<string, number>;\n  /** Average document length across the corpus. */\n  avgDocLen: number;\n  /** Total document count. */\n  totalDocs: number;\n}\n\n/** Precompute BM25 corpus statistics from the tokenised candidate set. */\nfunction buildCorpusStats(docs: string[][]): CorpusStats {\n  const docFreq = new Map<string, number>();\n  let totalLen = 0;\n  for (const tokens of docs) {\n    totalLen += tokens.length;\n    const unique = new Set(tokens);\n    for (const term of unique) docFreq.set(term, (docFreq.get(term) ?? 0) + 1);\n  }\n  const totalDocs = docs.length;\n  const avgDocLen = totalDocs > 0 ? totalLen / totalDocs : 0;\n  return { docFreq, avgDocLen, totalDocs };\n}\n\n/** BM25 saturation parameter; higher = slower term-frequency saturation. */\nconst BM25_K1 = 1.5;\n/** BM25 length normalisation strength; 0 disables, 1 is full normalisation. */\nconst BM25_B = 0.75;\n/** How much weight the original semantic score retains in the rerank tie-break. */\nconst BASE_SCORE_WEIGHT = 0.5;\n\n/** Compute BM25 score for one document against a tokenised query. */\nfunction bm25Score(queryTerms: string[], docTokens: string[], stats: CorpusStats): number {\n  if (docTokens.length === 0 || stats.totalDocs === 0) return 0;\n  const termFreq = countTerms(docTokens);\n  const lengthRatio = docTokens.length / (stats.avgDocLen || 1);\n\n  let total = 0;\n  for (const term of queryTerms) {\n    const tf = termFreq.get(term) ?? 0;\n    if (tf === 0) continue;\n    const idf = idfWeight(stats.docFreq.get(term) ?? 0, stats.totalDocs);\n    const numerator = tf * (BM25_K1 + 1);\n    const denominator = tf + BM25_K1 * (1 - BM25_B + BM25_B * lengthRatio);\n    total += idf * (numerator / denominator);\n  }\n  return total;\n}\n\n/** BM25 inverse-document-frequency component (Robertson-Spärck Jones form). */\nfunction idfWeight(docFrequency: number, totalDocs: number): number {\n  const numerator = totalDocs - docFrequency + 0.5;\n  const denominator = docFrequency + 0.5;\n  // +1 inside log keeps idf non-negative even when a term appears in every doc.\n  return Math.log(1 + numerator / denominator);\n}\n\n/** Count token occurrences in a single document. */\nfunction countTerms(tokens: string[]): Map<string, number> {\n  const counts = new Map<string, number>();\n  for (const token of tokens) counts.set(token, (counts.get(token) ?? 0) + 1);\n  return counts;\n}\n","/**\n * Review candidate persistence for the llmwiki compile pipeline.\n *\n * When `llmwiki compile --review` runs, generated wiki pages are routed\n * here as JSON candidate records under `.llmwiki/candidates/` instead of\n * being written directly to `wiki/`. Reviewers then approve or reject the\n * proposals via the `llmwiki review` subcommands.\n *\n * Candidates are deliberately kept as standalone JSON so they survive across\n * compile runs and can be inspected manually without the CLI. Each record\n * stores the full page body so approval is a pure copy — the LLM is never\n * called again at approval time.\n */\n\nimport { unlink } from \"fs/promises\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport { randomBytes } from \"crypto\";\nimport { atomicWrite, safeReadFile } from \"../utils/markdown.js\";\nimport {\n  listCandidateFileIds,\n  moveCandidateToArchive,\n} from \"../utils/candidate-store.js\";\nimport * as output from \"../utils/output.js\";\nimport {\n  CANDIDATES_DIR,\n  CANDIDATES_ARCHIVE_DIR,\n} from \"../utils/constants.js\";\nimport type { ReviewCandidate, SourceState } from \"../utils/types.js\";\nimport type { LintResult } from \"../linter/types.js\";\n\n/** Length (bytes) of the random suffix appended to candidate ids. */\nconst ID_SUFFIX_BYTES = 4;\n\n/** Filesystem extension used for candidate JSON files. */\nconst CANDIDATE_EXT = \".json\";\n\n/** Input shape for creating a new candidate (id + timestamp generated here). */\ninterface CandidateDraft {\n  title: string;\n  slug: string;\n  summary: string;\n  sources: string[];\n  body: string;\n  /**\n   * Per-source state entries to persist into `.llmwiki/state.json` when this\n   * candidate is approved. Keyed by source filename. Optional so callers that\n   * never need incremental tracking (legacy / tests) can omit it.\n   */\n  sourceStates?: Record<string, SourceState>;\n  /**\n   * Schema lint violations for the candidate body detected at compile time.\n   * Omit (or pass `undefined`) when the candidate body is clean.\n   */\n  schemaViolations?: LintResult[];\n  /**\n   * Provenance lint violations for the candidate body — malformed claim\n   * citations, out-of-bounds spans, or missing source files. Surfaced\n   * alongside schema violations so reviewers see citation issues before\n   * approving.\n   */\n  provenanceViolations?: LintResult[];\n}\n\n/** Build a deterministic-but-unique id from a slug and a short random suffix. */\nfunction buildCandidateId(slug: string): string {\n  const suffix = randomBytes(ID_SUFFIX_BYTES).toString(\"hex\");\n  return `${slug}-${suffix}`;\n}\n\n/** Absolute path to a candidate's JSON file. */\nfunction candidatePath(root: string, id: string): string {\n  return path.join(root, CANDIDATES_DIR, `${id}${CANDIDATE_EXT}`);\n}\n\n/** Absolute path to the archived JSON file for a rejected candidate. */\nfunction archivePath(root: string, id: string): string {\n  return path.join(root, CANDIDATES_ARCHIVE_DIR, `${id}${CANDIDATE_EXT}`);\n}\n\n/**\n * Persist a new candidate record and return it. The id is generated from the\n * slug plus a short random suffix so multiple compile runs can co-exist.\n * @param root - Project root directory.\n * @param draft - The candidate fields to persist.\n * @returns The full ReviewCandidate (with id + generatedAt populated).\n */\nexport async function writeCandidate(\n  root: string,\n  draft: CandidateDraft,\n): Promise<ReviewCandidate> {\n  const candidate: ReviewCandidate = {\n    id: buildCandidateId(draft.slug),\n    title: draft.title,\n    slug: draft.slug,\n    summary: draft.summary,\n    sources: draft.sources,\n    body: draft.body,\n    generatedAt: new Date().toISOString(),\n    ...(draft.sourceStates ? { sourceStates: draft.sourceStates } : {}),\n    ...(draft.schemaViolations ? { schemaViolations: draft.schemaViolations } : {}),\n    ...(draft.provenanceViolations ? { provenanceViolations: draft.provenanceViolations } : {}),\n  };\n\n  await atomicWrite(candidatePath(root, candidate.id), JSON.stringify(candidate, null, 2));\n  return candidate;\n}\n\n/**\n * Emit a CLI error, set exit code 1, and return null. Used by candidate load\n * helpers to avoid duplicating the error-path boilerplate.\n * @param message - Error message to display.\n */\nfunction failWithError(message: string): null {\n  output.status(\"!\", output.error(message));\n  process.exitCode = 1;\n  return null;\n}\n\n/**\n * Load a candidate by id and, if missing, emit the standard \"not found\" CLI\n * error and set process.exitCode = 1. Returns null when the candidate is\n * missing so callers can early-return without re-implementing the same\n * error block in every review subcommand.\n * @param root - Project root directory.\n * @param id - Candidate id to look up.\n */\nexport async function loadCandidateOrFail(\n  root: string,\n  id: string,\n): Promise<ReviewCandidate | null> {\n  const candidate = await readCandidate(root, id);\n  if (!candidate) return failWithError(`Candidate not found: ${id}`);\n  return candidate;\n}\n\n/**\n * Re-read a candidate under the lock and abort if it has disappeared.\n *\n * This is the authoritative TOCTOU guard: a concurrent approve or reject may\n * have removed the candidate after the pre-lock fast-fail but before the lock\n * was acquired. Returning `null` signals the caller to abort without writing\n * any output artefact.\n * @param root - Project root directory.\n * @param id - Candidate id to load.\n * @returns The candidate if still present, or `null` after setting exit code 1.\n */\nexport async function loadCandidateUnderLockOrFail(\n  root: string,\n  id: string,\n): Promise<ReviewCandidate | null> {\n  const candidate = await readCandidate(root, id);\n  if (!candidate) {\n    return failWithError(`Candidate ${id} was removed by another process during review.`);\n  }\n  return candidate;\n}\n\n/** Parse a single candidate JSON file. Returns null when the file is missing or malformed. */\nexport async function readCandidate(\n  root: string,\n  id: string,\n): Promise<ReviewCandidate | null> {\n  const raw = await safeReadFile(candidatePath(root, id));\n  if (!raw) return null;\n  try {\n    const parsed = JSON.parse(raw) as ReviewCandidate;\n    if (!isValidCandidate(parsed)) return null;\n    return parsed;\n  } catch {\n    return null;\n  }\n}\n\n/** Defensive type-guard so corrupted candidate files don't blow up the CLI. */\nfunction isValidCandidate(value: unknown): value is ReviewCandidate {\n  if (!value || typeof value !== \"object\") return false;\n  const candidate = value as Record<string, unknown>;\n  return (\n    typeof candidate.id === \"string\" &&\n    typeof candidate.title === \"string\" &&\n    typeof candidate.slug === \"string\" &&\n    typeof candidate.body === \"string\" &&\n    Array.isArray(candidate.sources)\n  );\n}\n\n/**\n * List every candidate currently pending review, sorted by generation time.\n * Skips files that aren't candidate JSON (e.g. the archive subdirectory).\n * @param root - Project root directory.\n * @returns All pending review candidates.\n */\nexport async function listCandidates(root: string): Promise<ReviewCandidate[]> {\n  const dir = path.join(root, CANDIDATES_DIR);\n  const ids = await listCandidateFileIds(dir);\n  const candidates: ReviewCandidate[] = [];\n  for (const id of ids) {\n    const candidate = await readCandidate(root, id);\n    if (candidate) candidates.push(candidate);\n  }\n\n  candidates.sort((a, b) => a.generatedAt.localeCompare(b.generatedAt));\n  return candidates;\n}\n\n/**\n * Count pending candidates using the same validity filter as listCandidates,\n * so consumers (e.g. `wiki_status.pendingCandidates`) never report counts\n * that disagree with what `review list` actually shows. Malformed JSON files\n * are skipped here exactly as they are by listCandidates.\n */\nexport async function countCandidates(root: string): Promise<number> {\n  const candidates = await listCandidates(root);\n  return candidates.length;\n}\n\n/** Remove a pending candidate from disk. Returns false when nothing existed to remove. */\nexport async function deleteCandidate(root: string, id: string): Promise<boolean> {\n  const filePath = candidatePath(root, id);\n  if (!existsSync(filePath)) return false;\n  await unlink(filePath);\n  return true;\n}\n\n/**\n * Move a candidate from the pending area into the archive subdirectory so\n * rejected proposals stay auditable without touching `wiki/`.\n * @param root - Project root directory.\n * @param id - Candidate id to archive.\n * @returns True when the candidate was found and archived.\n */\nexport async function archiveCandidate(root: string, id: string): Promise<boolean> {\n  return moveCandidateToArchive(candidatePath(root, id), archivePath(root, id));\n}\n","/**\n * Shared filesystem primitives for candidate queues.\n *\n * Both the concept review queue (`compiler/candidates.ts`) and the rule\n * candidate queue (`compiler/rule-candidates.ts`) persist one JSON file per\n * candidate under a directory, list those files, and move rejected records\n * into an archive subdirectory. These two operations were identical across the\n * queues; extracting them here removes the duplication while keeping each\n * queue's own id/shape logic local to its module.\n */\n\nimport { readdir, rename, unlink, writeFile, mkdir } from \"fs/promises\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport { safeReadFile } from \"./markdown.js\";\n\n/** Extension used for all candidate JSON files. */\nexport const CANDIDATE_JSON_EXT = \".json\";\n\n/**\n * Turn a dotted candidate id into a single filesystem-safe path segment.\n *\n * Only characters outside `[a-z0-9._-]` are replaced (with `_`); dots are\n * PRESERVED. Collapsing dots to `-` (the old behavior) made `rulecand.a.b-c`\n * and `rulecand.a-b.c` map to the same file, silently overwriting one\n * candidate with the other. Keeping dots makes the mapping injective for the\n * ids this codebase emits (category in `[a-z0-9_]`, slug in `[a-z0-9-]`).\n * @param candidateId - The dotted candidate id.\n */\nexport function candidateFileId(candidateId: string): string {\n  return candidateId.replace(/[^a-zA-Z0-9._-]/g, \"_\");\n}\n\n/**\n * List the file ids (basename without `.json`) of every candidate JSON file in\n * a directory, ignoring subdirectories (e.g. an `archive/` folder). Returns an\n * empty list when the directory does not exist.\n * @param dir - Absolute path to the candidate directory.\n */\nexport async function listCandidateFileIds(dir: string): Promise<string[]> {\n  if (!existsSync(dir)) return [];\n  const entries = await readdir(dir, { withFileTypes: true });\n  const ids: string[] = [];\n  for (const entry of entries) {\n    if (!entry.isFile() || !entry.name.endsWith(CANDIDATE_JSON_EXT)) continue;\n    ids.push(entry.name.slice(0, -CANDIDATE_JSON_EXT.length));\n  }\n  return ids;\n}\n\n/**\n * Move a candidate JSON file into an archive location, creating the archive\n * directory if needed. Falls back to copy + unlink when `rename` fails across\n * filesystems. Returns false when the source file does not exist.\n * @param sourcePath - Absolute path of the pending candidate file.\n * @param targetPath - Absolute archive destination path.\n */\nexport async function moveCandidateToArchive(\n  sourcePath: string,\n  targetPath: string,\n): Promise<boolean> {\n  if (!existsSync(sourcePath)) return false;\n  await mkdir(path.dirname(targetPath), { recursive: true });\n  try {\n    await rename(sourcePath, targetPath);\n  } catch {\n    const raw = await safeReadFile(sourcePath);\n    await writeFile(targetPath, raw, \"utf-8\");\n    await unlink(sourcePath);\n  }\n  return true;\n}\n","/**\n * Lint rules for wiki quality checks.\n *\n * Each rule is a function that takes a project root path and returns\n * an array of LintResult diagnostics. Rules perform pure static analysis\n * with no LLM calls — they inspect frontmatter, wikilinks, citations,\n * and file structure to find potential issues.\n */\n\nimport { readdir, readFile } from \"fs/promises\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport {\n  isMalformedCitationEntry,\n  parseFrontmatter,\n  parseProvenanceMetadata,\n  safeReadFile,\n  slugify,\n  splitCitationMarker,\n} from \"../utils/markdown.js\";\nimport {\n  CONCEPTS_DIR,\n  LOW_CONFIDENCE_THRESHOLD,\n  MAX_INFERRED_PARAGRAPHS_WITHOUT_CITATIONS,\n  QUERIES_DIR,\n  SOURCES_DIR,\n} from \"../utils/constants.js\";\nimport type { LintResult } from \"./types.js\";\nimport {\n  countWikilinks,\n  resolvePageKind,\n  type SchemaConfig,\n} from \"../schema/index.js\";\nimport { computeFreshness } from \"../freshness/index.js\";\nimport type { FreshnessSnapshot } from \"../freshness/types.js\";\n\n/** Minimum body length (in characters) for a page to be considered non-empty. */\nconst MIN_BODY_LENGTH = 50;\n\n/** Pattern matching [[Wikilink Title]] references in markdown content. */\nconst WIKILINK_PATTERN = /\\[\\[([^\\]]+)\\]\\]/g;\n\n/** Pattern matching ^[filename.md] citation markers in markdown content. */\nconst CITATION_PATTERN = /\\^\\[([^\\]]+)\\]/g;\n\n/** Match result with its line number and captured group. */\ninterface LineMatch {\n  captured: string;\n  line: number;\n}\n\n/**\n * Scan all lines of a page's content and return regex matches with line numbers.\n * Shared by rules that need to locate patterns within page bodies.\n */\nfunction findMatchesInContent(content: string, pattern: RegExp): LineMatch[] {\n  const results: LineMatch[] = [];\n  const lines = content.split(\"\\n\");\n  for (let i = 0; i < lines.length; i++) {\n    const matches = lines[i].matchAll(pattern);\n    for (const match of matches) {\n      results.push({ captured: match[1], line: i + 1 });\n    }\n  }\n  return results;\n}\n\n/**\n * Read all .md files from a directory, returning their paths and parsed content.\n * Returns an empty array if the directory does not exist.\n */\nasync function readMarkdownFiles(\n  dirPath: string,\n): Promise<Array<{ filePath: string; content: string }>> {\n  if (!existsSync(dirPath)) return [];\n\n  const entries = await readdir(dirPath);\n  const mdFiles = entries.filter((f) => f.endsWith(\".md\"));\n\n  const results = await Promise.all(\n    mdFiles.map(async (fileName) => {\n      const filePath = path.join(dirPath, fileName);\n      const content = await readFile(filePath, \"utf-8\");\n      return { filePath, content };\n    }),\n  );\n\n  return results;\n}\n\n/**\n * Collect all wiki pages from both concepts/ and queries/ directories.\n */\nexport async function collectAllPages(\n  root: string,\n): Promise<Array<{ filePath: string; content: string }>> {\n  const conceptPages = await readMarkdownFiles(path.join(root, CONCEPTS_DIR));\n  const queryPages = await readMarkdownFiles(path.join(root, QUERIES_DIR));\n  return [...conceptPages, ...queryPages];\n}\n\n/**\n * Build a set of slugs for all existing wiki pages.\n * Used to verify that wikilink targets actually exist.\n */\nfunction buildPageSlugSet(\n  pages: Array<{ filePath: string }>,\n): Set<string> {\n  const slugs = new Set<string>();\n  for (const page of pages) {\n    const baseName = path.basename(page.filePath, \".md\");\n    slugs.add(baseName.toLowerCase());\n  }\n  return slugs;\n}\n\n/** Find [[Title]] wikilinks that don't match any existing wiki page. */\nexport async function checkBrokenWikilinks(root: string): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const existingSlugs = buildPageSlugSet(pages);\n  const results: LintResult[] = [];\n\n  for (const page of pages) {\n    for (const { captured, line } of findMatchesInContent(page.content, WIKILINK_PATTERN)) {\n      const linkTarget = captured.split(\"|\")[0].trim();\n      const linkSlug = slugify(linkTarget);\n      if (!existingSlugs.has(linkSlug)) {\n        results.push({\n          rule: \"broken-wikilink\",\n          severity: \"error\",\n          file: page.filePath,\n          message: `Broken wikilink [[${captured}]] — no matching page found`,\n          line,\n        });\n      }\n    }\n  }\n\n  return results;\n}\n\n/** Find pages with `orphaned: true` in their frontmatter. */\nexport async function checkOrphanedPages(root: string): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const results: LintResult[] = [];\n\n  for (const page of pages) {\n    const { meta } = parseFrontmatter(page.content);\n    if (meta.orphaned === true) {\n      results.push({\n        rule: \"orphaned-page\",\n        severity: \"warning\",\n        file: page.filePath,\n        message: `Page is marked as orphaned`,\n      });\n    }\n  }\n\n  return results;\n}\n\n/**\n * Report pages whose computed freshness is actionable: `stale` (a source\n * changed since compile) or `orphaned` (every source it derived from was\n * deleted but no compile has cleaned the page up yet). Pages already flagged\n * `orphaned: true` in frontmatter are left to {@link checkOrphanedPages} so the\n * two rules never double-report. `fresh` and `unverified` are not findings —\n * unverified covers legitimately unowned pages (query pages, hand-authored\n * content) that should not warn. Receives the shared freshness snapshot so the\n * source-hash pass happens once per lint run.\n */\nexport async function checkStalePages(root: string, snapshot: FreshnessSnapshot): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const results: LintResult[] = [];\n  for (const page of pages) {\n    const { meta } = parseFrontmatter(page.content);\n    if (meta.orphaned === true) continue;\n    const slug = path.basename(page.filePath, \".md\");\n    const pageDirectory = path.basename(path.dirname(page.filePath)) === \"queries\" ? \"queries\" : \"concepts\";\n    const { freshnessStatus } = computeFreshness({ slug, pageDirectory, frontmatter: meta }, snapshot);\n    if (freshnessStatus === \"stale\") {\n      results.push({\n        rule: \"stale-page\",\n        severity: \"warning\",\n        file: page.filePath,\n        message: `Page is stale — a source it was compiled from has changed since the last compile`,\n      });\n    } else if (freshnessStatus === \"orphaned\") {\n      results.push({\n        rule: \"orphaned-page\",\n        severity: \"warning\",\n        file: page.filePath,\n        message: `Page is orphaned — every source it was compiled from has been deleted; recompile to clean it up`,\n      });\n    }\n  }\n  return results;\n}\n\n/** Find pages with empty or missing `summary` in frontmatter. */\nexport async function checkMissingSummaries(root: string): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const results: LintResult[] = [];\n\n  for (const page of pages) {\n    const { meta } = parseFrontmatter(page.content);\n    const summary = meta.summary;\n    const isMissing = !summary || (typeof summary === \"string\" && summary.trim() === \"\");\n\n    if (isMissing) {\n      results.push({\n        rule: \"missing-summary\",\n        severity: \"warning\",\n        file: page.filePath,\n        message: `Page has no summary in frontmatter`,\n      });\n    }\n  }\n\n  return results;\n}\n\n/** Find multiple pages whose titles match case-insensitively. */\nexport async function checkDuplicateConcepts(root: string): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const titleMap = new Map<string, string[]>();\n\n  for (const page of pages) {\n    const { meta } = parseFrontmatter(page.content);\n    const title = typeof meta.title === \"string\" ? meta.title : \"\";\n    if (!title) continue;\n\n    const normalizedTitle = title.toLowerCase().trim();\n    const existing = titleMap.get(normalizedTitle) ?? [];\n    existing.push(page.filePath);\n    titleMap.set(normalizedTitle, existing);\n  }\n\n  const results: LintResult[] = [];\n  for (const [title, files] of titleMap) {\n    if (files.length <= 1) continue;\n    for (const file of files) {\n      results.push({\n        rule: \"duplicate-concept\",\n        severity: \"error\",\n        file,\n        message: `Duplicate title \"${title}\" — also in ${files.filter((f) => f !== file).join(\", \")}`,\n      });\n    }\n  }\n\n  return results;\n}\n\n/** Find pages with frontmatter but very short or empty body content. */\nexport async function checkEmptyPages(root: string): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const results: LintResult[] = [];\n\n  for (const page of pages) {\n    const { meta, body } = parseFrontmatter(page.content);\n    const hasTitle = typeof meta.title === \"string\" && meta.title.trim() !== \"\";\n    const isBodyEmpty = body.trim().length < MIN_BODY_LENGTH;\n\n    if (hasTitle && isBodyEmpty) {\n      results.push({\n        rule: \"empty-page\",\n        severity: \"warning\",\n        file: page.filePath,\n        message: `Page body is empty or too short (< ${MIN_BODY_LENGTH} chars)`,\n      });\n    }\n  }\n\n  return results;\n}\n\n/** Strip an optional `:start-end` or `#Lstart-Lend` span suffix from a citation entry. */\nfunction stripSpanSuffix(entry: string): string {\n  const colonIdx = entry.indexOf(\":\");\n  const hashIdx = entry.indexOf(\"#\");\n  const cuts = [colonIdx, hashIdx].filter((i) => i >= 0);\n  if (cuts.length === 0) return entry;\n  return entry.slice(0, Math.min(...cuts));\n}\n\n/**\n * Flag pages whose frontmatter declares confidence below the threshold.\n * Pages without a confidence field are silently skipped to preserve\n * backward-compatibility with pre-existing wikis.\n */\nexport async function checkLowConfidencePages(root: string): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const results: LintResult[] = [];\n\n  for (const page of pages) {\n    const { meta } = parseFrontmatter(page.content);\n    const { confidence } = parseProvenanceMetadata(meta);\n    if (confidence === undefined || confidence >= LOW_CONFIDENCE_THRESHOLD) continue;\n    results.push({\n      rule: \"low-confidence\",\n      severity: \"warning\",\n      file: page.filePath,\n      message: `Page confidence ${confidence.toFixed(2)} is below ${LOW_CONFIDENCE_THRESHOLD}`,\n    });\n  }\n\n  return results;\n}\n\n/** Flag pages whose frontmatter records contradictions with other pages. */\nexport async function checkContradictedPages(root: string): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const results: LintResult[] = [];\n\n  for (const page of pages) {\n    const { meta } = parseFrontmatter(page.content);\n    const { contradictedBy } = parseProvenanceMetadata(meta);\n    if (!contradictedBy || contradictedBy.length === 0) continue;\n    const slugs = contradictedBy.map((r) => r.slug).join(\", \");\n    results.push({\n      rule: \"contradicted-page\",\n      severity: \"warning\",\n      file: page.filePath,\n      message: `Page contradicts: ${slugs}`,\n    });\n  }\n\n  return results;\n}\n\n/**\n * Flag pages with too many inferred paragraphs unsupported by direct\n * citations. Always derived from the rendered page body — the body is\n * the single source of truth, no metadata field is consulted. Earlier\n * versions trusted an LLM-estimated `inferredParagraphs` frontmatter\n * field, but that estimate was made before the page even existed and\n * routinely disagreed with what the model actually produced. Counting\n * uncited prose paragraphs in the rendered body matches what a\n * reviewer would see and survives hand-edits.\n */\nexport async function checkInferredWithoutCitations(root: string): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const results: LintResult[] = [];\n\n  for (const page of pages) {\n    const { body } = parseFrontmatter(page.content);\n    const inferred = countUncitedProseParagraphs(body);\n    if (inferred <= MAX_INFERRED_PARAGRAPHS_WITHOUT_CITATIONS) continue;\n    results.push({\n      rule: \"excess-inferred-paragraphs\",\n      severity: \"warning\",\n      file: page.filePath,\n      message: `Page has ${inferred} inferred paragraphs without citations (max ${MAX_INFERRED_PARAGRAPHS_WITHOUT_CITATIONS})`,\n    });\n  }\n\n  return results;\n}\n\n/**\n * Match a paragraph that looks like prose (not a heading, list, or code\n * block). Uses the Unicode `Letter` property so non-ASCII pages\n * generated via `--lang Chinese`, `--lang Japanese`, etc. (#46) are\n * still detected — the previous `[A-Za-z]` form silently dropped CJK,\n * Cyrillic, Greek, and Arabic prose, leaving\n * `excess-inferred-paragraphs` blind on those pages.\n */\nconst PROSE_PARAGRAPH_LEAD = /^\\p{L}/u;\n\n/** Count prose paragraphs in a body that lack a ^[citation] marker. */\nfunction countUncitedProseParagraphs(body: string): number {\n  const paragraphs = body.split(/\\n\\s*\\n/);\n  let count = 0;\n  for (const block of paragraphs) {\n    const trimmed = block.trim();\n    if (trimmed.length === 0) continue;\n    if (!PROSE_PARAGRAPH_LEAD.test(trimmed)) continue;\n    if (CITATION_PATTERN.test(trimmed)) {\n      CITATION_PATTERN.lastIndex = 0;\n      continue;\n    }\n    CITATION_PATTERN.lastIndex = 0;\n    count += 1;\n  }\n  return count;\n}\n\n/** Regex matching the `:start-end` span suffix on a citation entry. */\nconst COLON_SPAN_PATTERN = /^[^:#]+:(\\d+)(?:[,-]\\s*(\\d+))?$/;\n\n/** Regex matching the `#Lstart-Lend` span suffix on a citation entry. */\nconst HASH_SPAN_PATTERN = /^[^:#]+#L(\\d+)(?:-L(\\d+))?$/;\n\n/** Parsed line range from a citation entry, or null if no range is present. */\ninterface ParsedLineRange {\n  start: number;\n  end: number;\n}\n\n/**\n * Enforce per-kind cross-link minimums declared in the schema.\n * For each page, resolve its kind, look up the rule, and warn when the page\n * body has fewer wikilinks than the rule requires. Pages with kind `concept`\n * and a minimum of 0 (the default) generate no diagnostics, so existing\n * projects without a schema file see no behaviour change.\n *\n * Implementation delegates to {@link checkPageCrossLinks} per page so the\n * actual rule logic lives in exactly one place — the on-disk walker just\n * fans the per-page helper across `collectAllPages`.\n * @param root - Project root directory.\n * @param schema - Resolved schema config.\n */\nexport async function checkSchemaCrossLinks(\n  root: string,\n  schema: SchemaConfig,\n): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const results: LintResult[] = [];\n  for (const page of pages) {\n    results.push(...checkPageCrossLinks(page.content, page.filePath, schema));\n  }\n  return results;\n}\n\n/**\n * Check cross-link minimums for a single page given as a raw content string.\n *\n * Unlike `checkSchemaCrossLinks`, this function operates on content already in\n * memory without reading from disk. Used by the review pipeline to attach\n * schema violations to a candidate at write time so `review show` can surface\n * them before the reviewer approves the page.\n *\n * The `filePath` parameter is embedded verbatim in each `LintResult.file` so\n * callers control how the candidate is identified in diagnostic output.\n *\n * @param content - Full page content including frontmatter.\n * @param filePath - Logical file path to embed in diagnostics (may be virtual).\n * @param schema - Resolved schema config.\n * @returns Lint results for this single page, empty when no violations found.\n */\nexport function checkPageCrossLinks(\n  content: string,\n  filePath: string,\n  schema: SchemaConfig,\n): LintResult[] {\n  const { meta, body } = parseFrontmatter(content);\n  const kind = resolvePageKind(meta.kind, schema);\n  const rule = schema.kinds[kind];\n  if (rule.minWikilinks <= 0) return [];\n\n  const linkCount = countWikilinks(body);\n  if (linkCount >= rule.minWikilinks) return [];\n\n  return [\n    {\n      rule: \"schema-cross-link-minimum\",\n      severity: \"warning\",\n      file: filePath,\n      message:\n        `Page kind \"${kind}\" requires at least ${rule.minWikilinks} ` +\n        `[[wikilinks]] but only ${linkCount} found.`,\n    },\n  ];\n}\n\n/** Extract the line range from a citation entry string, or return null if there is none. */\nfunction parseLineRange(entry: string): ParsedLineRange | null {\n  const colonMatch = COLON_SPAN_PATTERN.exec(entry);\n  if (colonMatch) {\n    const start = Number(colonMatch[1]);\n    const end = colonMatch[2] !== undefined ? Number(colonMatch[2]) : start;\n    return { start, end };\n  }\n  const hashMatch = HASH_SPAN_PATTERN.exec(entry);\n  if (hashMatch) {\n    const start = Number(hashMatch[1]);\n    const end = hashMatch[2] !== undefined ? Number(hashMatch[2]) : start;\n    return { start, end };\n  }\n  return null;\n}\n\n/** Count the number of lines in a file's text content. */\nfunction countLines(content: string): number {\n  if (content.length === 0) return 0;\n  return content.split(\"\\n\").length;\n}\n\n/**\n * Find ^[filename.md] citations referencing source files that don't exist, and\n * flag claim-level spans whose line ranges exceed the source file's actual length.\n * Handles both single-source ^[file.md] and multi-source ^[a.md, b.md] forms,\n * plus the claim-level extension `^[file.md:42-58]` / `^[file.md#L42-L58]`.\n * Line counts are cached per source file to avoid redundant reads.\n */\nexport async function checkBrokenCitations(root: string): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const sourcesDir = path.join(root, SOURCES_DIR);\n  const results: LintResult[] = [];\n  const lineCountCache = new Map<string, number>();\n\n  for (const page of pages) {\n    const pageFindings = await checkPageBrokenCitations(\n      page.content,\n      page.filePath,\n      sourcesDir,\n      lineCountCache,\n    );\n    results.push(...pageFindings);\n  }\n\n  return results;\n}\n\n/**\n * Pure-body variant of {@link checkBrokenCitations} that inspects a single\n * page's content against an in-memory or on-disk sources directory. Used\n * by the on-disk lint walker above, and by the in-memory candidate-lint\n * path so `compile --review` surfaces broken-source-file and out-of-bounds\n * span findings before a reviewer approves the candidate.\n *\n * @param content - Full page markdown including frontmatter.\n * @param filePath - Logical path embedded in diagnostics (may be virtual).\n * @param sourcesDir - Absolute path to the project's sources/ directory.\n * @param lineCountCache - Optional cross-page cache; provide one when\n *   linting many pages so source file line counts aren't re-read.\n */\nexport async function checkPageBrokenCitations(\n  content: string,\n  filePath: string,\n  sourcesDir: string,\n  lineCountCache: Map<string, number> = new Map(),\n): Promise<LintResult[]> {\n  const results: LintResult[] = [];\n  for (const { captured, line } of findMatchesInContent(content, CITATION_PATTERN)) {\n    await collectBrokenForMarker(captured, line, filePath, sourcesDir, lineCountCache, results);\n  }\n  return results;\n}\n\n/** Append broken-citation diagnostics for every entry inside a single ^[...] marker. */\nasync function collectBrokenForMarker(\n  captured: string,\n  line: number,\n  pageFile: string,\n  sourcesDir: string,\n  lineCountCache: Map<string, number>,\n  out: LintResult[],\n): Promise<void> {\n  for (const part of splitCitationMarker(captured)) {\n    const trimmed = part.trim();\n    if (trimmed.length === 0) continue;\n    const filename = stripSpanSuffix(trimmed);\n    const citedPath = path.join(sourcesDir, filename);\n    if (!existsSync(citedPath)) {\n      out.push({\n        rule: \"broken-citation\",\n        severity: \"error\",\n        file: pageFile,\n        message: `Broken citation ^[${filename}] — source file not found`,\n        line,\n      });\n      continue;\n    }\n    const range = parseLineRange(trimmed);\n    if (range === null) continue;\n    const lineCount = await resolveLineCount(citedPath, filename, lineCountCache);\n    if (range.end <= lineCount) continue;\n    out.push({\n      rule: \"broken-citation\",\n      severity: \"error\",\n      file: pageFile,\n      message: `Claim-level span ^[${trimmed}] is out of bounds (source has only ${lineCount} lines)`,\n      line,\n    });\n  }\n}\n\n/** Return the line count for a source file, reading and caching if necessary. */\nasync function resolveLineCount(\n  citedPath: string,\n  filename: string,\n  cache: Map<string, number>,\n): Promise<number> {\n  const cached = cache.get(filename);\n  if (cached !== undefined) return cached;\n  const content = await safeReadFile(citedPath);\n  const lineCount = countLines(content);\n  cache.set(filename, lineCount);\n  return lineCount;\n}\n\n/**\n * Find ^[...] markers whose entries do not parse against the documented\n * paragraph or claim-level grammar (e.g. `^[file.md:abc]` or `^[file.md#X]`).\n * Detects malformed claim-level citations without breaking the paragraph form.\n */\nexport async function checkMalformedClaimCitations(root: string): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const results: LintResult[] = [];\n  for (const page of pages) {\n    results.push(...checkPageMalformedCitations(page.content, page.filePath));\n  }\n  return results;\n}\n\n/**\n * Pure-body variant of {@link checkMalformedClaimCitations} that inspects\n * a single page's content. Used by both the on-disk lint walker above and\n * the in-memory candidate-lint path so `compile --review` surfaces\n * malformed claim citations before a reviewer approves the candidate.\n */\nexport function checkPageMalformedCitations(content: string, filePath: string): LintResult[] {\n  const results: LintResult[] = [];\n  for (const { captured, line } of findMatchesInContent(content, CITATION_PATTERN)) {\n    for (const part of splitCitationMarker(captured)) {\n      if (!isMalformedCitationEntry(part)) continue;\n      results.push({\n        rule: \"malformed-claim-citation\",\n        severity: \"error\",\n        file: filePath,\n        message: `Malformed claim citation ^[${captured}] — expected file.md, file.md:N-N, or file.md#LN-LN`,\n        line,\n      });\n    }\n  }\n  return results;\n}\n","/**\n * Computed source-freshness layer.\n *\n * Derives a page's freshness on demand from a FreshnessSnapshot (state.json\n * hashes + current source hashes). Pure — never reads or writes the filesystem\n * and never persists freshness. See localdocs/specs/2026-06-04-source-freshness-design.md.\n */\n\nimport type { FreshnessSnapshot, PageFreshness, PageFreshnessInput, FreshnessStatus, SourceFreshness } from \"./types.js\";\nimport { existsSync } from \"fs\";\nimport { realpath } from \"fs/promises\";\nimport path from \"path\";\nimport { readStateClassified } from \"../utils/state.js\";\nimport type { ClassifiedState } from \"../utils/state.js\";\nimport { hashFile } from \"../compiler/hasher.js\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\n\n/** Compute the three orthogonal freshness signals for one page. */\nexport function computeFreshness(page: PageFreshnessInput, snapshot: FreshnessSnapshot): PageFreshness {\n  return {\n    freshnessStatus: classify(page, snapshot),\n    contradicted: Array.isArray(page.frontmatter.contradictedBy) && page.frontmatter.contradictedBy.length > 0,\n    archived: page.frontmatter.archived === true,\n  };\n}\n\n/** Source-derived freshness status, per the spec's ordered ownership algorithm. */\nfunction classify(page: PageFreshnessInput, snapshot: FreshnessSnapshot): FreshnessStatus {\n  if (snapshot.stateStatus !== \"ok\") return \"unverified\";\n  // Query pages are generated answers, not source projections — always unverified,\n  // never orphaned/fresh (they also never receive `orphaned` frontmatter).\n  if (page.pageDirectory === \"queries\") return \"unverified\";\n  if (page.frontmatter.orphaned === true) return \"orphaned\";\n\n  const owners = ownersOf(page.slug, snapshot);\n  if (owners.length === 0) return \"unverified\";\n\n  const live = owners.filter((o) => o.exists);\n  if (live.length === 0) return \"orphaned\";\n  if (live.length < owners.length) return \"stale\";\n  if (live.some((o) => o.currentHash !== o.recordedHash)) return \"stale\";\n  return \"fresh\";\n}\n\n/** Sources whose recorded concept set includes this page's slug (state is authoritative). */\nfunction ownersOf(slug: string, snapshot: FreshnessSnapshot) {\n  return Object.values(snapshot.sources).filter((s) => s.concepts.includes(slug));\n}\n\n/**\n * Build the per-run freshness snapshot: one read-only state read + one hash\n * pass over sources/. Shared by every freshness consumer so hashing happens once.\n *\n * @param classified - Optional pre-read classified state. When supplied the\n *   disk read is skipped, letting callers that already have state avoid a\n *   redundant read. Omit (or pass `undefined`) to read from disk as usual.\n */\nexport async function buildFreshnessSnapshot(\n  root: string,\n  classified?: ClassifiedState,\n): Promise<FreshnessSnapshot> {\n  const { status, state } = classified ?? (await readStateClassified(root));\n  const sources: FreshnessSnapshot[\"sources\"] = {};\n  if (status === \"ok\") {\n    const sourcesRoot = path.resolve(root, SOURCES_DIR);\n    // Resolve the real sources root ONCE — the per-source containment check reuses it,\n    // so a snapshot over N sources does at most N (not 2N) realpath syscalls.\n    const realSourcesRoot = await realSourcesRootOrFallback(sourcesRoot);\n    for (const [file, entry] of Object.entries(state.sources)) {\n      sources[file] = await classifySource(sourcesRoot, realSourcesRoot, file, entry);\n    }\n  }\n  return { stateStatus: status, sources };\n}\n\n/**\n * Real path of the sources root, falling back to the lexical path if realpath\n * throws (e.g. sources/ does not exist yet). The fallback is safe: a missing\n * sources root means no source file can resolve inside it, and per-file\n * existsSync already gates hashing.\n */\nasync function realSourcesRootOrFallback(sourcesRoot: string): Promise<string> {\n  try {\n    return await realpath(sourcesRoot);\n  } catch {\n    return sourcesRoot;\n  }\n}\n\n/**\n * Resolve a file's symlinks and check whether its real path is inside the\n * pre-resolved real sources root. The root is realpath'd once by the caller so\n * projects under symlinked temp dirs (e.g. macOS /tmp → /private/tmp) still pass.\n * Returns false on any error (treat as not inside, refuse to hash).\n */\nasync function resolvesInsideSources(resolved: string, realSourcesRoot: string): Promise<boolean> {\n  try {\n    const realFile = await realpath(resolved);\n    return realFile === realSourcesRoot || realFile.startsWith(realSourcesRoot + path.sep);\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Classify one source entry from state.json, guarding against both path traversal\n * and symlink escapes. A poisoned key like `../../etc/passwd` is rejected by the\n * cheap lexical check (first gate). A symlink inside sources/ pointing outside is\n * rejected by the realpath check (second gate). Both cases return exists:false.\n */\nasync function classifySource(\n  sourcesRoot: string,\n  realSourcesRoot: string,\n  file: string,\n  entry: { hash: string; concepts: string[] },\n): Promise<SourceFreshness> {\n  const resolved = path.resolve(sourcesRoot, file);\n  const lexicallyInside = resolved === sourcesRoot || resolved.startsWith(sourcesRoot + path.sep);\n  if (!lexicallyInside) {\n    return { recordedHash: entry.hash, currentHash: null, exists: false, concepts: entry.concepts };\n  }\n  const exists = existsSync(resolved);\n  if (exists && !(await resolvesInsideSources(resolved, realSourcesRoot))) {\n    // Symlink escapes sources/ — treat as unverifiable, never hash/read it.\n    return { recordedHash: entry.hash, currentHash: null, exists: false, concepts: entry.concepts };\n  }\n  return {\n    recordedHash: entry.hash,\n    currentHash: exists ? await hashFile(resolved) : null,\n    exists,\n    concepts: entry.concepts,\n  };\n}\n","/**\n * Wiki page rendering for the llmwiki compile pipeline.\n *\n * Encapsulates the single-page generation step: gather related pages, call\n * the LLM, build frontmatter, and produce the final markdown blob. Splitting\n * this away from the orchestrator (`compiler/index.ts`) keeps the orchestrator\n * focused on phase sequencing and lets the review-candidate code path reuse\n * the exact same renderer used for direct writes.\n */\n\nimport { readdir } from \"fs/promises\";\nimport path from \"path\";\nimport {\n  buildFrontmatter,\n  parseFrontmatter,\n  safeReadFile,\n} from \"../utils/markdown.js\";\nimport { callClaude } from \"../utils/llm.js\";\nimport { buildPagePrompt } from \"./prompts.js\";\nimport { addObsidianMeta } from \"./obsidian.js\";\nimport { addModelProvenanceMeta, addProvenanceMeta, reportContradictionWarnings } from \"./provenance.js\";\nimport { CONCEPTS_DIR } from \"../utils/constants.js\";\nimport type { SchemaConfig } from \"../schema/index.js\";\nimport type { ExtractedConcept } from \"../utils/types.js\";\n\n/** Maximum number of existing concept pages to include as cross-reference context. */\nconst RELATED_PAGE_CONTEXT_LIMIT = 5;\n\n/** A merged-concept input from the orchestrator (multiple sources merged into one). */\ninterface RenderableConcept {\n  slug: string;\n  concept: ExtractedConcept;\n  sourceFiles: string[];\n  combinedContent: string;\n}\n\n/**\n * Render a wiki page (frontmatter + body) for a merged concept by calling\n * the LLM with cross-referencing context from existing concept pages.\n * @param root - Project root directory.\n * @param entry - The merged concept to render.\n * @param schema - Resolved schema config, used to stamp `kind` on frontmatter.\n * @returns Full markdown content (frontmatter + body, trailing newline).\n */\nexport async function renderMergedPageContent(\n  root: string,\n  entry: RenderableConcept,\n  schema: SchemaConfig,\n): Promise<string> {\n  const pagePath = path.join(root, CONCEPTS_DIR, `${entry.slug}.md`);\n  const existingPage = await safeReadFile(pagePath);\n  const relatedPages = await loadRelatedPages(root, entry.slug);\n\n  const system = buildPagePrompt(\n    entry.concept.concept,\n    entry.combinedContent,\n    existingPage,\n    relatedPages,\n  );\n\n  const pageBody = await callClaude({\n    system,\n    messages: [\n      { role: \"user\", content: `Write the wiki page for \"${entry.concept.concept}\".` },\n    ],\n  });\n\n  const frontmatter = buildMergedFrontmatter(entry, existingPage, schema);\n  reportContradictionWarnings(entry.concept.concept, entry.concept);\n  return `${frontmatter}\\n\\n${pageBody}\\n`;\n}\n\n/**\n * Construct the frontmatter block for a merged concept, preserving createdAt\n * and stamping the `kind` field from the schema's default kind.\n */\nfunction buildMergedFrontmatter(\n  entry: RenderableConcept,\n  existingPage: string,\n  schema: SchemaConfig,\n): string {\n  const now = new Date().toISOString();\n  const existing = existingPage ? parseFrontmatter(existingPage) : null;\n  const createdAt = (existing?.meta.createdAt && typeof existing.meta.createdAt === \"string\")\n    ? existing.meta.createdAt\n    : now;\n  const frontmatterFields: Record<string, unknown> = {\n    title: entry.concept.concept,\n    summary: entry.concept.summary,\n    sources: entry.sourceFiles,\n    kind: schema.defaultKind,\n    createdAt,\n    updatedAt: now,\n  };\n  addObsidianMeta(frontmatterFields, entry.concept.concept, entry.concept.tags ?? []);\n  addProvenanceMeta(frontmatterFields, entry.concept);\n  addModelProvenanceMeta(frontmatterFields);\n  return buildFrontmatter(frontmatterFields);\n}\n\n/**\n * Load related wiki pages to provide cross-referencing context.\n * Returns concatenated content of up to RELATED_PAGE_CONTEXT_LIMIT pages.\n * @param root - Project root directory.\n * @param excludeSlug - Slug of the current page to exclude.\n * @returns Concatenated related page contents (empty when concepts dir is missing).\n */\nasync function loadRelatedPages(root: string, excludeSlug: string): Promise<string> {\n  const conceptsPath = path.join(root, CONCEPTS_DIR);\n  let files: string[];\n\n  try {\n    files = await readdir(conceptsPath);\n  } catch {\n    return \"\";\n  }\n\n  const related = files\n    .filter((f) => f.endsWith(\".md\") && f !== `${excludeSlug}.md`)\n    .slice(0, RELATED_PAGE_CONTEXT_LIMIT);\n\n  const contents: string[] = [];\n  for (const f of related) {\n    const content = await safeReadFile(path.join(conceptsPath, f));\n    if (!content) continue;\n    const { meta } = parseFrontmatter(content);\n    if (meta.orphaned) continue;\n    contents.push(content);\n  }\n\n  return contents.join(\"\\n\\n---\\n\\n\");\n}\n","/**\n * Commander action for `llmwiki query <question>`.\n * Two-step LLM-powered wiki query that first selects relevant pages from the\n * wiki index, then streams an answer grounded in those pages. Optionally saves\n * the response as a new page in wiki/queries/.\n *\n * Step 1 - Page Selection: Reads wiki/index.md and asks Claude (via tool_use)\n * to pick the most relevant concept pages for the question.\n *\n * Step 2 - Answer Generation: Loads the selected pages in full and streams\n * a cited answer to the terminal.\n */\n\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport { callClaude } from \"../utils/llm.js\";\nimport type { LLMTool } from \"../utils/provider.js\";\nimport { atomicWrite, safeReadFile, slugify, buildFrontmatter, parseFrontmatter } from \"../utils/markdown.js\";\nimport { languageDirective } from \"../utils/output-language.js\";\nimport { generateIndex } from \"../compiler/indexgen.js\";\nimport * as output from \"../utils/output.js\";\nimport {\n  QUERY_PAGE_LIMIT,\n  INDEX_FILE,\n  CONCEPTS_DIR,\n  QUERIES_DIR,\n  CHUNK_TOP_K,\n  CHUNK_RERANK_KEEP,\n} from \"../utils/constants.js\";\nimport {\n  findRelevantPages,\n  findRelevantChunks,\n  updateEmbeddings,\n  type ChunkEmbeddingEntry,\n} from \"../utils/embeddings.js\";\nimport { rerankWithBm25 } from \"../utils/retrieval.js\";\nimport { appendLog, formatWikilinkList } from \"../utils/activity-log.js\";\nimport type { ChunkCitation, QueryResult, RetrievalDebug } from \"../utils/types.js\";\n\n/** Directories to search when loading selected pages, in priority order. */\nconst PAGE_DIRS = [CONCEPTS_DIR, QUERIES_DIR];\n\n/** Tool schema for page selection (provider-agnostic). */\nconst PAGE_SELECTION_TOOL: LLMTool = {\n  name: \"select_pages\",\n  description: \"Select the most relevant wiki pages to answer a question\",\n  input_schema: {\n    type: \"object\" as const,\n    properties: {\n      pages: {\n        type: \"array\",\n        items: {\n          type: \"string\",\n          description: \"Slug of a relevant wiki page (e.g. 'llm-knowledge-bases')\",\n        },\n        maxItems: QUERY_PAGE_LIMIT,\n      },\n      reasoning: {\n        type: \"string\",\n        description: \"Brief explanation of why these pages were selected\",\n      },\n    },\n    required: [\"pages\", \"reasoning\"],\n  },\n};\n\ninterface PageSelectionResult {\n  pages: string[];\n  reasoning: string;\n}\n\n/**\n * Select the most relevant wiki pages for a question using Claude tool_use.\n * @param question - The user's natural language question.\n * @param indexContent - The full text of wiki/index.md.\n * @returns Parsed page slugs and reasoning from Claude.\n */\nexport async function selectPages(\n  question: string,\n  indexContent: string,\n): Promise<PageSelectionResult> {\n  const systemPrompt =\n    \"You are a knowledge base assistant. Given a question and a wiki index, select the most relevant pages.\";\n\n  const userMessage = `Question: ${question}\\n\\nWiki Index:\\n${indexContent}`;\n\n  const rawResult = await callClaude({\n    system: systemPrompt,\n    messages: [{ role: \"user\", content: userMessage }],\n    tools: [PAGE_SELECTION_TOOL],\n  });\n\n  try {\n    const parsed = JSON.parse(rawResult);\n    return {\n      pages: Array.isArray(parsed.pages) ? parsed.pages.filter((p: unknown) => typeof p === \"string\") : [],\n      reasoning: typeof parsed.reasoning === \"string\" ? parsed.reasoning : \"No reasoning provided\",\n    };\n  } catch {\n    return { pages: [], reasoning: \"Failed to parse page selection response\" };\n  }\n}\n\n/** Render a list of candidate pages in the same bullet format selectPages() consumes. */\nfunction buildFilteredIndex(\n  candidates: Array<{ slug: string; title: string; summary: string }>,\n): string {\n  return candidates\n    .map((entry) => `- **${entry.slug}**: ${entry.title} — ${entry.summary}`)\n    .join(\"\\n\");\n}\n\ninterface SelectedPages {\n  pages: string[];\n  rawPages: string[];\n  reasoning: string;\n  /** Chunk citations driving the selection — empty when chunk store is absent. */\n  chunks: ChunkCitation[];\n  /** Debug snapshot of the retrieval pipeline (only populated in debug mode). */\n  debug?: RetrievalDebug;\n}\n\n/**\n * Pick relevant pages using a chunk-aware embedding pre-filter when available,\n * falling back to page-level embeddings, then to sending the full wiki index.\n */\nasync function selectRelevantPages(\n  root: string,\n  question: string,\n  debug: boolean,\n): Promise<SelectedPages> {\n  const chunkSelection = await trySelectViaChunks(root, question, debug);\n  if (chunkSelection) return chunkSelection;\n\n  const candidates = await tryFindRelevantPages(root, question);\n\n  if (candidates.length > 0) {\n    const filteredIndex = buildFilteredIndex(candidates);\n    const { pages: rawPages, reasoning } = await selectPages(question, filteredIndex);\n    // Tool output holds slugs directly in the semantic path — no slugify needed.\n    return { pages: rawPages, rawPages, reasoning, chunks: [] };\n  }\n\n  const indexContent = await safeReadFile(path.join(root, INDEX_FILE));\n  const { pages: rawPages, reasoning } = await selectPages(question, indexContent);\n  return { pages: rawPages.map((p) => slugify(p)), rawPages, reasoning, chunks: [] };\n}\n\n/**\n * Attempt chunk-level retrieval + reranking. Returns null when no chunk store\n * is available (caller falls back to page-level retrieval transparently).\n */\nasync function trySelectViaChunks(\n  root: string,\n  question: string,\n  debug: boolean,\n): Promise<SelectedPages | null> {\n  const ranked = await tryFindRelevantChunks(root, question);\n  if (ranked.length === 0) return null;\n\n  const reranked = rerankWithBm25(\n    question,\n    ranked.map(({ chunk, score }) => ({ text: chunk.text, baseScore: score, chunk })),\n  );\n  const kept = reranked.slice(0, CHUNK_RERANK_KEEP);\n  const reorderingHappened = wasReordered(ranked, kept.map((k) => k.candidate.chunk));\n  const chunkCitations = toChunkCitations(kept);\n  const pageSlugs = collapseToPages(chunkCitations, QUERY_PAGE_LIMIT);\n  const reasoning = buildChunkReasoning(chunkCitations, pageSlugs);\n\n  return {\n    pages: pageSlugs,\n    rawPages: pageSlugs,\n    reasoning,\n    chunks: chunkCitations,\n    debug: debug ? buildDebug(chunkCitations, pageSlugs, reorderingHappened) : undefined,\n  };\n}\n\n/** Detect whether reranking actually changed the chunk order. */\nfunction wasReordered(\n  before: Array<{ chunk: ChunkEmbeddingEntry }>,\n  after: ChunkEmbeddingEntry[],\n): boolean {\n  const limit = Math.min(before.length, after.length);\n  for (let i = 0; i < limit; i++) {\n    if (before[i].chunk !== after[i]) return true;\n  }\n  return false;\n}\n\ninterface RankedChunk {\n  candidate: { chunk: ChunkEmbeddingEntry };\n  score: number;\n}\n\n/** Convert reranked candidates into citation records consumed downstream. */\nfunction toChunkCitations(ranked: RankedChunk[]): ChunkCitation[] {\n  return ranked.map(({ candidate, score }) => ({\n    slug: candidate.chunk.slug,\n    title: candidate.chunk.title,\n    chunkIndex: candidate.chunk.chunkIndex,\n    score,\n    text: candidate.chunk.text,\n  }));\n}\n\n/** Collapse chunk citations down to a deduplicated list of parent page slugs. */\nfunction collapseToPages(chunks: ChunkCitation[], limit: number): string[] {\n  const slugs: string[] = [];\n  const seen = new Set<string>();\n  for (const chunk of chunks) {\n    if (seen.has(chunk.slug)) continue;\n    seen.add(chunk.slug);\n    slugs.push(chunk.slug);\n    if (slugs.length >= limit) break;\n  }\n  return slugs;\n}\n\n/** Human-readable reasoning trail for the chunk-driven selection. */\nfunction buildChunkReasoning(chunks: ChunkCitation[], pages: string[]): string {\n  const top = chunks.slice(0, pages.length);\n  const summary = top.map((c) => `${c.slug}#${c.chunkIndex} (${c.score.toFixed(3)})`).join(\", \");\n  return `Selected ${pages.length} page(s) from ${chunks.length} reranked chunks: ${summary}`;\n}\n\n/** Snapshot used by debug mode — pure data, no side-effects. */\nfunction buildDebug(\n  chunks: ChunkCitation[],\n  pageSlugs: string[],\n  reranked: boolean,\n): RetrievalDebug {\n  const bestPerPage = new Map<string, number>();\n  for (const c of chunks) {\n    const prev = bestPerPage.get(c.slug);\n    if (prev === undefined || c.score > prev) bestPerPage.set(c.slug, c.score);\n  }\n  return {\n    pages: pageSlugs.map((slug) => ({ slug, score: bestPerPage.get(slug) ?? 0 })),\n    chunks,\n    usedChunks: true,\n    reranked,\n  };\n}\n\n/** Chunk-level candidate lookup that never throws. */\nasync function tryFindRelevantChunks(\n  root: string,\n  question: string,\n): Promise<Array<{ chunk: ChunkEmbeddingEntry; score: number }>> {\n  try {\n    return await findRelevantChunks(root, question, CHUNK_TOP_K);\n  } catch (err) {\n    const message = err instanceof Error ? err.message : String(err);\n    output.status(\"!\", output.dim(`Chunk pre-filter unavailable (${message}); falling back.`));\n    return [];\n  }\n}\n\n/** Embedding-based candidate lookup that never throws. */\nasync function tryFindRelevantPages(\n  root: string,\n  question: string,\n): Promise<Array<{ slug: string; title: string; summary: string }>> {\n  try {\n    return await findRelevantPages(root, question);\n  } catch (err) {\n    const message = err instanceof Error ? err.message : String(err);\n    output.status(\"!\", output.dim(`Semantic pre-filter unavailable (${message}); using full index.`));\n    return [];\n  }\n}\n\n/**\n * Load the full content of each selected wiki page.\n * Skips pages that don't exist and warns the user.\n * @param root - Absolute path to the project root directory.\n * @param slugs - Array of page slugs to load from wiki/concepts/.\n * @returns Combined page contents with slug headers for context.\n */\nexport async function loadSelectedPages(root: string, slugs: string[]): Promise<string> {\n  const sections: string[] = [];\n\n  for (const slug of slugs) {\n    let content = \"\";\n    for (const dir of PAGE_DIRS) {\n      const candidate = await safeReadFile(path.join(root, dir, `${slug}.md`));\n      if (!candidate) continue;\n      const { meta } = parseFrontmatter(candidate);\n      if (meta.orphaned) continue;\n      content = candidate;\n      break;\n    }\n\n    if (!content) {\n      output.status(\"?\", output.warn(`Page not found: ${slug}.md — skipping`));\n      continue;\n    }\n\n    sections.push(`--- Page: ${slug} ---\\n${content}`);\n  }\n\n  return sections.join(\"\\n\\n\");\n}\n\n/** Base system prompt body. The output-language directive is appended at call time. */\nconst ANSWER_SYSTEM_PROMPT_BASE =\n  \"You are a knowledge assistant. Answer the question using ONLY the wiki content provided. \" +\n  \"Cite specific pages using [[Page Title]] wikilinks. \" +\n  \"If the wiki doesn't contain enough information, say so.\";\n\n/**\n * Build the answer-generation system prompt, appending the configured\n * output-language directive when present (issue #37).\n */\nfunction buildAnswerSystemPrompt(): string {\n  const lang = languageDirective();\n  return lang ? `${ANSWER_SYSTEM_PROMPT_BASE} ${lang}` : ANSWER_SYSTEM_PROMPT_BASE;\n}\n\n/**\n * Call the LLM with the loaded wiki pages as grounding context. When chunk\n * citations are available, they are attached as a \"Most relevant excerpts\"\n * section so the model can prioritise the precise paragraphs that drove\n * page selection.\n */\nasync function callAnswerLLM(\n  question: string,\n  pagesContent: string,\n  chunks: ChunkCitation[],\n  onToken?: (text: string) => void,\n): Promise<string> {\n  const provenance = chunks.length > 0 ? buildChunkProvenance(chunks) : \"\";\n  const userMessage =\n    `Question: ${question}\\n\\nRelevant wiki pages:\\n${pagesContent}${provenance}`;\n  return callClaude({\n    system: buildAnswerSystemPrompt(),\n    messages: [{ role: \"user\", content: userMessage }],\n    stream: Boolean(onToken),\n    onToken,\n  });\n}\n\n/** Render the top chunk excerpts as a labelled section appended to the prompt. */\nfunction buildChunkProvenance(chunks: ChunkCitation[]): string {\n  const sections = chunks.map(\n    (chunk) => `--- ${chunk.slug} (chunk ${chunk.chunkIndex}) ---\\n${chunk.text}`,\n  );\n  return `\\n\\nMost relevant excerpts (from chunk-level retrieval):\\n${sections.join(\"\\n\\n\")}`;\n}\n\n/**\n * Generate a one-line summary from the answer for use in the wiki index.\n * Takes the first sentence (up to 120 chars) so the page-selection LLM\n * has retrieval signal beyond just the title.\n * @param answer - The full answer text.\n * @returns A short summary string.\n */\nexport function summarizeAnswer(answer: string): string {\n  const firstLine = answer.trim().split(/\\n/)[0] ?? \"\";\n  const firstSentence = firstLine.split(/(?<=[.!?])\\s/)[0] ?? firstLine;\n  return firstSentence.slice(0, 120);\n}\n\n/**\n * Save a query answer as a wiki page in the queries/ directory,\n * then regenerate the wiki index so the answer is immediately retrievable.\n * @param root - Absolute path to the project root directory.\n * @param question - The original question used as the page title.\n * @param answer - The generated answer body.\n */\nasync function saveQueryPage(root: string, question: string, answer: string): Promise<string> {\n  const slug = slugify(question);\n  const filePath = path.join(root, QUERIES_DIR, `${slug}.md`);\n\n  const frontmatter = buildFrontmatter({\n    title: question,\n    summary: summarizeAnswer(answer),\n    type: \"query\",\n    createdAt: new Date().toISOString(),\n  });\n\n  const document = `${frontmatter}\\n\\n${answer}\\n`;\n  await atomicWrite(filePath, document);\n\n  output.status(\n    \"+\",\n    output.success(`Saved query → ${output.source(filePath)}`),\n  );\n\n  // Regenerate the index so the saved query is immediately discoverable\n  // by the next query's page-selection step.\n  await generateIndex(root);\n\n  // Index the new query so semantic search retrieves it on the next question.\n  // Non-critical: embedding failures (e.g. missing VOYAGE_API_KEY) don't block save.\n  try {\n    await updateEmbeddings(root, [slug]);\n  } catch (err) {\n    const message = err instanceof Error ? err.message : String(err);\n    output.status(\"!\", output.warn(`Skipped embeddings update: ${message}`));\n  }\n\n  return slug;\n}\n\n/** Options for generateAnswer — programmatic-friendly. */\ninterface GenerateAnswerOptions {\n  /** Persist the answer as a wiki query page when set. */\n  save?: boolean;\n  /** Per-token callback for streaming. Omit for non-streaming usage. */\n  onToken?: (text: string) => void;\n  /** Callback fired once page selection completes — lets CLIs print reasoning before streaming. */\n  onPageSelection?: (pages: string[], reasoning: string) => void;\n  /** Capture chunk-level provenance + scoring detail in the result. */\n  debug?: boolean;\n}\n\n/**\n * Run the two-step page-selection + answer-generation pipeline and return\n * a structured QueryResult. This is the programmatic entry point used by\n * the MCP server and any non-CLI consumer.\n *\n * @param root - Absolute path to the project root directory.\n * @param question - The natural language question to answer.\n * @param options - Streaming + save behaviour controls.\n * @returns Answer text, selected slugs, reasoning, and saved slug if applicable.\n */\nexport async function generateAnswer(\n  root: string,\n  question: string,\n  options: GenerateAnswerOptions = {},\n): Promise<QueryResult> {\n  if (!existsSync(path.join(root, INDEX_FILE))) {\n    throw new Error(\"Wiki index not found. Run `llmwiki compile` first.\");\n  }\n\n  const selection = await selectRelevantPages(root, question, Boolean(options.debug));\n  options.onPageSelection?.(selection.pages, selection.reasoning);\n\n  const pagesContent = await loadSelectedPages(root, selection.pages);\n\n  if (!pagesContent) {\n    return buildEmptyResult(selection);\n  }\n\n  const answer = await callAnswerLLM(question, pagesContent, selection.chunks, options.onToken);\n  const saved = options.save ? await saveQueryPage(root, question, answer) : undefined;\n\n  // Journal the query only after the answer is produced — matching compile,\n  // which logs after finalization — so a mid-flight LLM failure records nothing.\n  // Logged here (not in the CLI command) so MCP queries are captured too.\n  await appendLog(root, \"query\", question, {\n    details: selection.pages.length > 0 ? [`Pages: ${formatWikilinkList(selection.pages)}`] : [],\n  });\n\n  return {\n    answer,\n    selectedPages: selection.pages,\n    reasoning: selection.reasoning,\n    saved,\n    debug: selection.debug,\n  };\n}\n\n/** Build the empty-pages result while preserving any debug/chunk context. */\nfunction buildEmptyResult(selection: SelectedPages): QueryResult {\n  return {\n    answer: \"\",\n    selectedPages: selection.pages,\n    reasoning: selection.reasoning,\n    debug: selection.debug,\n  };\n}\n\n/**\n * Run a two-step LLM-powered query against the knowledge wiki.\n * @param root - Absolute path to the project root directory.\n * @param question - The natural language question to answer.\n * @param options - Command options (e.g. --save to persist the answer).\n */\nexport default async function queryCommand(\n  root: string,\n  question: string,\n  options: { save?: boolean; debug?: boolean },\n): Promise<void> {\n  if (!existsSync(path.join(root, INDEX_FILE))) {\n    output.status(\"!\", output.error(\"Wiki index not found. Run `llmwiki compile` first.\"));\n    return;\n  }\n\n  output.header(\"Selecting relevant pages\");\n\n  const result = await generateAnswer(root, question, {\n    save: options.save,\n    debug: options.debug,\n    onToken: (text) => process.stdout.write(text),\n    onPageSelection: (pages, reasoning) => {\n      output.status(\"i\", output.dim(`Reasoning: ${reasoning}`));\n      output.status(\"*\", output.info(`Selected ${pages.length} page(s): ${pages.join(\", \")}`));\n      output.header(\"Generating answer\");\n    },\n  });\n\n  // Newline after streamed answer so subsequent terminal output formats cleanly.\n  process.stdout.write(\"\\n\");\n\n  if (result.debug) printDebugSnapshot(result.debug);\n\n  if (!result.answer) {\n    output.status(\"!\", output.error(\"No matching pages found. Try refining your question.\"));\n    return;\n  }\n\n  if (result.saved) {\n    output.status(\"→\", output.dim(\"Saved. Future queries will use this answer as context.\"));\n  } else {\n    output.status(\"→\", output.dim(\"Tip: use --save to add this answer to your wiki\"));\n  }\n}\n\n/** Render the retrieval debug snapshot to the terminal for human inspection. */\nfunction printDebugSnapshot(debug: RetrievalDebug): void {\n  output.header(\"Retrieval debug\");\n  output.status(\n    \"i\",\n    output.dim(\n      `Source: ${debug.usedChunks ? \"chunk-level\" : \"page-level\"}; ` +\n      `reranked: ${debug.reranked ? \"yes\" : \"no\"}`,\n    ),\n  );\n  for (const page of debug.pages) {\n    output.status(\"•\", `${page.slug} (best chunk score ${page.score.toFixed(3)})`);\n  }\n  for (const chunk of debug.chunks) {\n    const preview = chunk.text.slice(0, DEBUG_CHUNK_PREVIEW_CHARS).replace(/\\s+/g, \" \").trim();\n    output.status(\n      \"·\",\n      output.dim(`${chunk.slug}#${chunk.chunkIndex} score=${chunk.score.toFixed(3)} :: ${preview}…`),\n    );\n  }\n}\n\n/** Maximum chunk preview length printed in --debug output. */\nconst DEBUG_CHUNK_PREVIEW_CHARS = 120;\n","/**\n * Wiki linter orchestrator.\n *\n * Imports all lint rules, runs them concurrently, and aggregates\n * results into a summary with error/warning/info counts.\n * This is the main entry point for programmatic lint access.\n */\n\nimport type { LintResult, LintRule, LintSummary, SchemaAwareLintRule } from \"./types.js\";\nimport {\n  checkBrokenWikilinks,\n  checkOrphanedPages,\n  checkMissingSummaries,\n  checkDuplicateConcepts,\n  checkEmptyPages,\n  checkBrokenCitations,\n  checkMalformedClaimCitations,\n  checkLowConfidencePages,\n  checkContradictedPages,\n  checkInferredWithoutCitations,\n  checkSchemaCrossLinks,\n  checkStalePages,\n} from \"./rules.js\";\nimport { loadSchema } from \"../schema/index.js\";\nimport { buildFreshnessSnapshot } from \"../freshness/index.js\";\nimport type { FreshnessSnapshot } from \"../freshness/types.js\";\n\n/** Rule-only lint checks that don't depend on the schema layer. */\nconst RULES_WITHOUT_SCHEMA: LintRule[] = [\n  checkBrokenWikilinks,\n  checkOrphanedPages,\n  checkMissingSummaries,\n  checkDuplicateConcepts,\n  checkEmptyPages,\n  checkBrokenCitations,\n  checkMalformedClaimCitations,\n  checkLowConfidencePages,\n  checkContradictedPages,\n  checkInferredWithoutCitations,\n];\n\n/** Lint rules that need the resolved schema to know per-kind expectations. */\nconst RULES_WITH_SCHEMA: SchemaAwareLintRule[] = [checkSchemaCrossLinks];\n\ntype FreshnessLintRule = (root: string, snapshot: FreshnessSnapshot) => Promise<LintResult[]>;\nconst RULES_WITH_FRESHNESS: FreshnessLintRule[] = [checkStalePages];\n\n/**\n * Count occurrences of a specific severity level in the results.\n */\nfunction countBySeverity(\n  results: LintResult[],\n  severity: LintResult[\"severity\"],\n): number {\n  return results.filter((r) => r.severity === severity).length;\n}\n\n/**\n * Run all lint rules concurrently against the wiki at the given root.\n * Loads the project schema (or defaults) so schema-aware rules can enforce\n * per-kind cross-link minimums alongside structural checks.\n * @param root - Absolute path to the project root directory.\n * @returns A summary containing all diagnostics and severity counts.\n */\nexport async function lint(root: string): Promise<LintSummary> {\n  const schema = await loadSchema(root);\n  const freshness = await buildFreshnessSnapshot(root);\n  const [plainResults, schemaResults, freshnessResults] = await Promise.all([\n    Promise.all(RULES_WITHOUT_SCHEMA.map((rule) => rule(root))),\n    Promise.all(RULES_WITH_SCHEMA.map((rule) => rule(root, schema))),\n    Promise.all(RULES_WITH_FRESHNESS.map((rule) => rule(root, freshness))),\n  ]);\n\n  const results = [...plainResults.flat(), ...schemaResults.flat(), ...freshnessResults.flat()];\n\n  const summary: LintSummary = {\n    errors: countBySeverity(results, \"error\"),\n    warnings: countBySeverity(results, \"warning\"),\n    info: countBySeverity(results, \"info\"),\n    results,\n  };\n\n  // lint is intentionally not journaled to log.md — it is a read-only check,\n  // and the MCP `lint_wiki` tool documents it as non-mutating.\n  return summary;\n}\n","/**\n * Build the frozen-at-startup `ViewerSnapshot` consumed by every viewer\n * endpoint. Every count, page list, and index payload that the HTTP\n * layer needs is captured here exactly once — v1 deliberately does not\n * live-watch the filesystem, so post-startup mutations are intentionally\n * invisible to the running viewer until it restarts.\n *\n * The snapshot consolidates five data sources:\n *   - `collectViewerPages` for the decorated page list AND the\n *     concept/query counts (deriving counts from the already-confined\n *     page list means symlinked entries dropped by the collector\n *     cannot quietly inflate the counts via a second unconfined scan)\n *   - `readStateClassified` (read-only, never writes a `.bak`) for the\n *     compiled-source count AND as the input to the freshness snapshot\n *   - `buildFreshnessSnapshot` for per-page freshness and the aggregate\n *     stale/orphaned counts (one state read + one hash pass over sources/)\n *   - `countCandidates` for the pending-reviews count\n *   - `readdir(sources/)` for the cheap source-file count\n */\n\nimport { readdir, readFile, realpath } from \"fs/promises\";\nimport path from \"path\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\nimport { countCandidates } from \"../compiler/candidates.js\";\nimport { readStateClassified } from \"../utils/state.js\";\nimport { collectViewerPages, resolveBareSlugList } from \"./collect.js\";\nimport { extractWikilinkSlugs } from \"../wiki/collect.js\";\nimport { isMalformedCitationEntry } from \"../utils/markdown.js\";\nimport { buildGraphData } from \"./graph.js\";\nimport { buildFreshnessSnapshot, computeFreshness } from \"../freshness/index.js\";\nimport type { FreshnessSnapshot } from \"../freshness/types.js\";\nimport type {\n  ViewerCounts,\n  ViewerIndex,\n  ViewerPage,\n  ViewerProject,\n  ViewerRecentPage,\n  ViewerSnapshot,\n  ViewerWarning,\n} from \"./types.js\";\n\nconst RECENT_PAGES_LIMIT = 8;\nconst INDEX_HREF = \"/#/index\";\n\n/**\n * Build the immutable startup snapshot for a project root. Reads pages,\n * counts, source state, candidates, and the optional `wiki/index.md`\n * exactly once and returns a fully populated `ViewerSnapshot`. Callers\n * must NOT re-derive any of these from disk on a per-request path —\n * `readLintCache` in `src/viewer/health.ts` is the sole exception.\n */\nexport async function buildViewerSnapshot(root: string): Promise<ViewerSnapshot> {\n  const [pages, classified, pendingReviews, sourceFilenames, index] = await Promise.all([\n    collectViewerPages(root),\n    readStateClassified(root),\n    countCandidates(root),\n    listSourceFiles(root),\n    readIndexFile(root),\n  ]);\n  const freshnessSnapshot = await buildFreshnessSnapshot(root, classified);\n  const project = buildProject(root);\n  const fullIndex: ViewerIndex = {\n    available: index.available,\n    href: INDEX_HREF,\n    body: index.body,\n    outgoingLinks: resolveBareSlugList(extractWikilinkSlugs(index.body), pages),\n  };\n  const sourceFileSet = new Set(sourceFilenames);\n  // Concept/query counts are derived from `pages`, the already-confined\n  // viewer page list, NOT from a second unconfined directory scan.\n  // Anything the collector dropped for path-safety reasons (symlinked\n  // file or directory) is therefore also excluded from the counts.\n  const annotatedPages = pages\n    .map((page) => annotateCitationWarnings(page, sourceFileSet))\n    .map((page) => attachFreshness(page, freshnessSnapshot));\n  const counts = buildCounts(annotatedPages, sourceFilenames, pendingReviews, classified.state);\n  const graph = buildGraphData(annotatedPages);\n  return {\n    root,\n    generatedAt: new Date().toISOString(),\n    stateStatus: classified.status,\n    project,\n    counts,\n    index: fullIndex,\n    recentPages: buildRecentPages(annotatedPages),\n    pages: annotatedPages,\n    sourceFilenames,\n    graph,\n  };\n}\n\n/**\n * Append `unresolved_citation` and `malformed_citation` warnings to a\n * page based on its parsed citations and the project's source-file\n * list. Slice 1 only produced parser-level warnings; citation\n * resolvability needs the snapshot's source-file list, so this is the\n * earliest layer that can decide.\n *\n * The body is re-scanned for raw `^[…]` markers (rather than iterating\n * `page.citations`) because `extractClaimCitations` drops citations\n * whose ONLY entry has an invalid line range — but those still need a\n * `malformed_citation` warning. Scanning the body gives every marker a\n * chance to be classified.\n */\nfunction annotateCitationWarnings(page: ViewerPage, sourceFiles: ReadonlySet<string>): ViewerPage {\n  const extra: ViewerWarning[] = [];\n  const markerPattern = /\\^\\[([^\\]\\n]+)\\]/g;\n  let match: RegExpExecArray | null;\n  while ((match = markerPattern.exec(page.body)) !== null) {\n    appendCitationWarningsForMarker(match[1], sourceFiles, extra);\n  }\n  if (extra.length === 0) return page;\n  return { ...page, warnings: [...page.warnings, ...extra] };\n}\n\n/**\n * Derive the frozen counts from the annotated page list, source filenames,\n * candidates count, and state. Concept/query counts are derived from pages\n * (the already-confined collector list) so symlinked drops don't inflate them.\n */\nfunction buildCounts(\n  pages: ViewerPage[],\n  sourceFilenames: string[],\n  pendingReviews: number,\n  state: { sources: Record<string, unknown> },\n): ViewerCounts {\n  return {\n    concepts: pages.filter((p) => p.pageDirectory === \"concepts\").length,\n    queries: pages.filter((p) => p.pageDirectory === \"queries\").length,\n    sourceFiles: sourceFilenames.length,\n    pendingReviews,\n    compiledSources: Object.keys(state.sources).length,\n    stale: pages.filter((p) => p.freshness.freshnessStatus === \"stale\").length,\n    orphaned: pages.filter((p) => p.freshness.freshnessStatus === \"orphaned\").length,\n  };\n}\n\n/**\n * Attach computed source-freshness to a page. Called once per page during\n * snapshot build so freshness is frozen at startup alongside all other\n * snapshot data.\n */\nfunction attachFreshness(page: ViewerPage, snapshot: FreshnessSnapshot): ViewerPage {\n  return {\n    ...page,\n    freshness: computeFreshness(\n      { slug: page.slug, pageDirectory: page.pageDirectory, frontmatter: page.frontmatter },\n      snapshot,\n    ),\n  };\n}\n\n/** Classify every comma-separated entry inside one `^[…]` marker. */\nfunction appendCitationWarningsForMarker(\n  raw: string,\n  sourceFiles: ReadonlySet<string>,\n  into: ViewerWarning[],\n): void {\n  for (const entry of raw.split(\",\")) {\n    const trimmed = entry.trim();\n    if (trimmed.length === 0) continue;\n    if (isMalformedCitationEntry(trimmed)) {\n      into.push({\n        code: \"malformed_citation\",\n        message: `Malformed citation entry: ${trimmed}`,\n      });\n      continue;\n    }\n    const file = trimmed.split(/[:#]/)[0];\n    if (file.length > 0 && !sourceFiles.has(file)) {\n      into.push({\n        code: \"unresolved_citation\",\n        message: `Source not found: ${file}`,\n      });\n    }\n  }\n}\n\n\n/** Project title and bare directory name for the dashboard header. */\nfunction buildProject(root: string): ViewerProject {\n  const rootName = path.basename(root);\n  return { title: rootName, rootName };\n}\n\n/**\n * List filenames directly under `sources/`. Returns an empty array when\n * the directory is missing. The Slice 4 citation renderer uses this list\n * to mark each chip `data-resolved` without per-request directory scans;\n * `counts.sourceFiles` is the cheap `.length` of the same list.\n *\n * Stricter than \"stays under project root\": `realpath(<root>/sources)`\n * must equal the literal canonical path `<canonicalRoot>/sources`. A\n * symlinked `sources/` directory — even pointing in-root — returns an\n * empty list, matching the same containment posture the wiki collector\n * uses for `wiki/concepts/` and `wiki/queries/`. Symlinked entries\n * inside the directory are excluded by `Dirent.isFile()` (which returns\n * false for symlinks since `withFileTypes` does not follow them).\n */\nasync function listSourceFiles(root: string): Promise<string[]> {\n  let canonicalRoot: string;\n  try {\n    canonicalRoot = await realpath(root);\n  } catch {\n    return [];\n  }\n  const expectedDir = path.join(canonicalRoot, SOURCES_DIR);\n  let realDir: string;\n  try {\n    realDir = await realpath(expectedDir);\n  } catch {\n    return [];\n  }\n  if (realDir !== expectedDir) return [];\n  try {\n    const entries = await readdir(realDir, { withFileTypes: true });\n    return entries.filter((e) => e.isFile()).map((e) => e.name);\n  } catch {\n    return [];\n  }\n}\n\n/**\n * Read `wiki/index.md` if present. Missing index is not an error: many\n * projects compile without an index page, and the viewer renders an\n * \"index unavailable\" placeholder for the `/#/index` route.\n *\n * Stricter than \"stays under project root\": `realpath(wiki/index.md)`\n * must equal the literal canonical path `<root>/wiki/index.md`. A\n * symlinked `wiki/index.md` is treated as unavailable, even when the\n * link target also lives inside the project — pointing the index at\n * (say) `<root>/README.md` would let the index endpoint render\n * content that has no business being the project's compiled index.\n * A symlinked `wiki/` directory is dropped by the same equality check.\n */\nasync function readIndexFile(root: string): Promise<{ available: boolean; body: string }> {\n  let canonicalRoot: string;\n  try {\n    canonicalRoot = await realpath(root);\n  } catch {\n    return { available: false, body: \"\" };\n  }\n  const expectedIndex = path.join(canonicalRoot, \"wiki\", \"index.md\");\n  let resolved: string;\n  try {\n    resolved = await realpath(expectedIndex);\n  } catch {\n    return { available: false, body: \"\" };\n  }\n  if (resolved !== expectedIndex) {\n    return { available: false, body: \"\" };\n  }\n  try {\n    const body = await readFile(resolved, \"utf-8\");\n    return { available: true, body };\n  } catch {\n    return { available: false, body: \"\" };\n  }\n}\n\n/**\n * Top-N recently updated pages for the dashboard. Pages without an\n * `updatedAt` frontmatter field sort to the end with an empty string so\n * the list remains deterministic.\n */\nfunction buildRecentPages(pages: ViewerPage[]): ViewerRecentPage[] {\n  const rows: ViewerRecentPage[] = pages.map((page) => ({\n    id: page.id,\n    pageDirectory: page.pageDirectory,\n    slug: page.slug,\n    title: page.title,\n    updatedAt:\n      typeof page.frontmatter.updatedAt === \"string\" ? (page.frontmatter.updatedAt as string) : \"\",\n  }));\n  rows.sort((a, b) => b.updatedAt.localeCompare(a.updatedAt));\n  return rows.slice(0, RECENT_PAGES_LIMIT);\n}\n\n","/**\n * Shared low-level wiki page collector.\n *\n * Walks `wiki/concepts/` and `wiki/queries/`, derives the slug from each\n * filename stem (NOT through `slugify()` — filename slugs are the canonical\n * filesystem-truth identifier; slugifying them would shift routes, exports,\n * and citation lookups), parses frontmatter via `parseFrontmatterStatus`,\n * and returns one `RawWikiPage` per readable `.md` file with a `parseStatus`\n * field describing structural problems.\n *\n * Content semantics: this layer does not drop pages for parse-level\n * failures (missing frontmatter, malformed YAML, missing title, orphaned\n * flag). Those are surfaced as `parseStatus` flags so the caller decides.\n *\n * Path-safety: this layer DOES drop entries that fail confinement to\n * their expected canonical directory. Specifically — a symlinked\n * `wiki/concepts/` directory (even pointing in-root), a symlinked\n * `.md` file whose `realpath` resolves anywhere other than under the\n * expected concepts/queries directory, and any unreadable entry — are\n * silently excluded. Two callers consume it:\n *\n *   - `src/export/collect.ts` filters on `parseStatus.orphaned` and\n *     `parseStatus.hasTitle` to preserve the existing export semantics.\n *   - `src/viewer/collect.ts` retains every record and maps `parseStatus`\n *     flags into `ViewerWarning` objects so users can diagnose malformed\n *     pages in the UI.\n */\n\nimport { readdir, readFile } from \"fs/promises\";\nimport path from \"path\";\nimport { parseFrontmatterStatus, slugify } from \"../utils/markdown.js\";\nimport { CONCEPTS_DIR, QUERIES_DIR } from \"../utils/constants.js\";\nimport type { PageDirectory } from \"../export/types.js\";\nimport { safeRealpath, isInsideDir } from \"../utils/path-confine.js\";\n\n/** Regex that matches `[[wikilink]]` or `[[wikilink|alias]]` patterns. */\nconst WIKILINK_RE = /\\[\\[([^\\]|]+)(?:\\|([^\\]]+))?\\]\\]/g;\n\n/**\n * Structural status of a single page's frontmatter, surfaced to callers so\n * they can decide whether to filter, warn, or pass through.\n */\ninterface RawPageParseStatus {\n  /** True when the file begins with a `---\\n…\\n---` block. */\n  hasFrontmatterBlock: boolean;\n  /** True when the frontmatter block exists but YAML failed to parse. */\n  malformedFrontmatter: boolean;\n  /** True when frontmatter contains a non-empty string `title`. */\n  hasTitle: boolean;\n  /** True when frontmatter explicitly sets `orphaned: true`. */\n  orphaned: boolean;\n}\n\n/**\n * Raw page record returned by the shared collector. Lower-level than\n * `ExportPage` or `ViewerPage`: no decoration, no filtering, no warnings.\n */\nexport interface RawWikiPage {\n  /** Filename stem (filename without the trailing `.md`). */\n  slug: string;\n  /** Which wiki/ subdirectory the page came from. */\n  pageDirectory: PageDirectory;\n  /** Absolute path on disk, useful for diagnostics and editor links. */\n  filePath: string;\n  /** Title from frontmatter when present; undefined otherwise. */\n  title?: string;\n  /** Parsed frontmatter (empty object when missing or malformed). */\n  frontmatter: Record<string, unknown>;\n  /** Markdown body with the frontmatter block stripped. */\n  body: string;\n  /** Structural status flags consumed by export and viewer callers. */\n  parseStatus: RawPageParseStatus;\n}\n\n/**\n * Extract the slugs of all pages linked via `[[wikilinks]]` in the body.\n * Wikilink targets ARE slugified — the human-typed link text may not match\n * the on-disk filename verbatim, so we normalize to the same shape `slugify`\n * produces. Returns deduplicated targets.\n */\nexport function extractWikilinkSlugs(body: string): string[] {\n  const slugs = new Set<string>();\n  WIKILINK_RE.lastIndex = 0;\n  let match: RegExpExecArray | null;\n  while ((match = WIKILINK_RE.exec(body)) !== null) {\n    slugs.add(slugify(match[1].trim()));\n  }\n  return [...slugs];\n}\n\n/**\n * Like `extractWikilinkSlugs` but also preserves the original human-typed\n * text for each target. Used to give dangling-link ghost nodes a readable\n * title instead of a slugified identifier.\n */\nexport function extractWikilinkTargets(body: string): { slug: string; display: string }[] {\n  const seen = new Set<string>();\n  const targets: { slug: string; display: string }[] = [];\n  WIKILINK_RE.lastIndex = 0;\n  let match: RegExpExecArray | null;\n  while ((match = WIKILINK_RE.exec(body)) !== null) {\n    const target = match[1].trim();\n    const alias = match[2]?.trim();\n    const slug = slugify(target);\n    const display = alias ?? target;\n    if (!seen.has(slug)) {\n      seen.add(slug);\n      targets.push({ slug, display });\n    }\n  }\n  return targets;\n}\n\n/**\n * Parse a single markdown file into a `RawWikiPage`. Returns null only when\n * the file cannot be read — every other failure mode (missing frontmatter,\n * malformed YAML, missing title, orphaned flag) is preserved as a\n * `parseStatus` flag so the caller decides how to handle it.\n */\nasync function parsePageFile(\n  filePath: string,\n  slug: string,\n  pageDirectory: PageDirectory,\n): Promise<RawWikiPage | null> {\n  let raw: string;\n  try {\n    raw = await readFile(filePath, \"utf-8\");\n  } catch {\n    return null;\n  }\n\n  const { meta, body, hasFrontmatterBlock, malformedFrontmatter } = parseFrontmatterStatus(raw);\n  const title = typeof meta.title === \"string\" && meta.title.length > 0 ? meta.title : undefined;\n  return {\n    slug,\n    pageDirectory,\n    filePath,\n    title,\n    frontmatter: meta,\n    body,\n    parseStatus: {\n      hasFrontmatterBlock,\n      malformedFrontmatter,\n      hasTitle: title !== undefined,\n      orphaned: meta.orphaned === true,\n    },\n  };\n}\n\n/**\n * Collect every readable `.md` file from a single wiki subdirectory.\n *\n * Confinement is stricter than \"stays under project root\": the\n * directory itself must resolve via `realpath` to the exact expected\n * path under `canonicalRoot` (so a symlinked `wiki/concepts/` is\n * skipped wholesale even when its target is also inside the project),\n * and each `.md` entry must resolve to a path under that canonical\n * expected directory (so a symlinked `wiki/concepts/leak.md` pointing\n * at `<root>/README.md` or `<root>/wiki/queries/x.md` is dropped).\n */\nasync function collectFromDir(\n  canonicalRoot: string,\n  pageDirectory: PageDirectory,\n  subdir: string,\n): Promise<RawWikiPage[]> {\n  const expectedDir = path.join(canonicalRoot, subdir);\n  const realDir = await safeRealpath(expectedDir);\n  if (realDir !== expectedDir) return [];\n  let files: string[];\n  try {\n    files = await readdir(realDir);\n  } catch {\n    return [];\n  }\n  const pages: RawWikiPage[] = [];\n  for (const file of files.filter((f) => f.endsWith(\".md\"))) {\n    const candidate = path.join(realDir, file);\n    const resolved = await safeRealpath(candidate);\n    if (!resolved || !isInsideDir(resolved, realDir)) continue;\n    const slug = file.replace(/\\.md$/, \"\");\n    const page = await parsePageFile(resolved, slug, pageDirectory);\n    if (page) pages.push(page);\n  }\n  return pages;\n}\n\n/**\n * Collect all readable wiki pages from `wiki/concepts/` and `wiki/queries/`.\n * Entries dropped for path-safety reasons (see `collectFromDir`) are\n * silently excluded. Pages are returned in filesystem order within each\n * directory, with concepts before queries; callers that need a stable\n * total order should sort.\n */\nexport async function collectRawWikiPages(root: string): Promise<RawWikiPage[]> {\n  const canonicalRoot = await safeRealpath(root);\n  if (!canonicalRoot) return [];\n  const [concepts, queries] = await Promise.all([\n    collectFromDir(canonicalRoot, \"concepts\", CONCEPTS_DIR),\n    collectFromDir(canonicalRoot, \"queries\", QUERIES_DIR),\n  ]);\n  return [...concepts, ...queries];\n}\n","/**\n * Viewer-facing page collector.\n *\n * Consumes the structural records produced by `src/wiki/collect.ts` and\n * decorates each one with the fields the HTTP server needs:\n *   - namespaced `id` (`concepts/<slug>` or `queries/<slug>`)\n *   - `outgoingLinks` resolved against the in-memory page list using the\n *     bare-slug precedence rule (concepts win over queries)\n *   - `citations` extracted via `extractClaimCitations`\n *   - stable `ViewerWarning` objects derived from `parseStatus` flags\n *\n * Unlike the export collector, this layer never drops a page: pages with\n * missing or malformed frontmatter are retained with a warning so users\n * can navigate to them and see what is wrong.\n */\n\nimport { collectRawWikiPages, extractWikilinkSlugs, extractWikilinkTargets } from \"../wiki/collect.js\";\nimport type { RawWikiPage } from \"../wiki/collect.js\";\nimport { extractClaimCitations, slugify } from \"../utils/markdown.js\";\nimport type { PageId, ViewerPage, ViewerWarning } from \"./types.js\";\nimport type { PageFreshness } from \"../freshness/types.js\";\n\n/** Minimal page shape `resolveBareSlug` needs to find a target. */\ntype PageIndexEntry = {\n  id: PageId;\n  pageDirectory: ViewerPage[\"pageDirectory\"];\n  slug: string;\n  /** Declared frontmatter aliases, used as a resolution fallback after exact slug. */\n  aliases?: readonly string[];\n};\n\n/**\n * Build the decorated page list for a project root. Each `ViewerPage`\n * carries its namespaced id, resolved outgoing links, citations, and any\n * `ViewerWarning` objects derived from the underlying `parseStatus` flags.\n * Returns pages in collector order (concepts then queries).\n */\nexport async function collectViewerPages(root: string): Promise<ViewerPage[]> {\n  const raw = await collectRawWikiPages(root);\n  return decoratePages(raw);\n}\n\n/**\n * Resolve a bare-slug wikilink target to a namespaced `PageId`. The\n * precedence rule (concepts before queries) matches the spec and is the\n * same logic used for both per-page outgoing links and `/api/index` link\n * resolution; exporting it here keeps callers from re-implementing the\n * order and accidentally diverging.\n */\nexport function resolveBareSlug(\n  slug: string,\n  pages: ReadonlyArray<PageIndexEntry>,\n): PageId | null {\n  if (slug.length === 0) return null;\n  const concept = pages.find((p) => p.pageDirectory === \"concepts\" && p.slug === slug);\n  if (concept) return concept.id;\n  const query = pages.find((p) => p.pageDirectory === \"queries\" && p.slug === slug);\n  if (query) return query.id;\n  // Alias fallback: a page whose declared aliases slugify to this target. An\n  // exact slug match always wins (above) so a real page is never shadowed by\n  // another page's alias; concepts still take precedence over queries.\n  const conceptAlias = pages.find((p) => p.pageDirectory === \"concepts\" && hasAliasSlug(p, slug));\n  if (conceptAlias) return conceptAlias.id;\n  const queryAlias = pages.find((p) => p.pageDirectory === \"queries\" && hasAliasSlug(p, slug));\n  if (queryAlias) return queryAlias.id;\n  return null;\n}\n\n/** True when any of the page's declared aliases slugifies to `slug`. */\nfunction hasAliasSlug(page: PageIndexEntry, slug: string): boolean {\n  return (page.aliases ?? []).some((alias) => slugify(alias) === slug);\n}\n\n/**\n * Resolve a list of bare-slug wikilink targets against an in-memory page\n * index and deduplicate the resulting `PageId`s while preserving first-\n * occurrence order. Unresolved targets are dropped.\n */\nexport function resolveBareSlugList(\n  targets: string[],\n  pages: ReadonlyArray<PageIndexEntry>,\n): PageId[] {\n  const seen = new Set<PageId>();\n  const ordered: PageId[] = [];\n  for (const target of targets) {\n    const resolved = resolveBareSlug(target, pages);\n    if (resolved && !seen.has(resolved)) {\n      seen.add(resolved);\n      ordered.push(resolved);\n    }\n  }\n  return ordered;\n}\n\n/**\n * Two-pass decoration: build the namespaced id/title/warnings shell for\n * every page first, then resolve wikilink targets against the completed\n * shell. Single-pass would let a page miss links to pages later in the\n * list; the index has to be complete before resolution begins.\n */\nfunction decoratePages(raw: RawWikiPage[]): ViewerPage[] {\n  const shells = raw.map(buildPageShell);\n  for (const page of shells) {\n    const slugTargets = extractWikilinkSlugs(page.body);\n    const richTargets = extractWikilinkTargets(page.body);\n    page.outgoingLinks = resolveBareSlugList(slugTargets, shells);\n    page.danglingLinks = collectDanglingLinks(richTargets, shells);\n  }\n  return shells;\n}\n\n/**\n * Return targets from `targets` that `resolveBareSlug` could not find,\n * deduplicated by slug and in first-occurrence order.\n */\nfunction collectDanglingLinks(\n  targets: { slug: string; display: string }[],\n  pages: ReadonlyArray<PageIndexEntry>,\n): { slug: string; display: string }[] {\n  const seen = new Set<string>();\n  const dangling: { slug: string; display: string }[] = [];\n  for (const t of targets) {\n    if (resolveBareSlug(t.slug, pages) === null && !seen.has(t.slug)) {\n      seen.add(t.slug);\n      dangling.push(t);\n    }\n  }\n  return dangling;\n}\n\n/**\n * Build the parts of a `ViewerPage` that do not need cross-page resolution\n * (id, title, citations, warnings). `outgoingLinks` starts empty and is\n * filled in once every shell is built.\n */\nfunction buildPageShell(page: RawWikiPage): ViewerPage {\n  const id: PageId = `${page.pageDirectory}/${page.slug}`;\n  return {\n    id,\n    slug: page.slug,\n    pageDirectory: page.pageDirectory,\n    title: page.title ?? page.slug,\n    filePath: page.filePath,\n    frontmatter: page.frontmatter,\n    body: page.body,\n    aliases: readAliases(page.frontmatter),\n    outgoingLinks: [],\n    citations: extractClaimCitations(page.body),\n    warnings: warningsFromParseStatus(page),\n    // Placeholder: overwritten by attachFreshness() in buildViewerSnapshot.\n    freshness: UNVERIFIED_FRESHNESS,\n  };\n}\n\n/** Default freshness placeholder — overwritten in the snapshot build. */\nconst UNVERIFIED_FRESHNESS: PageFreshness = {\n  freshnessStatus: \"unverified\",\n  contradicted: false,\n  archived: false,\n};\n\n/** Read the `aliases` frontmatter field as a string list (empty when absent/malformed). */\nfunction readAliases(frontmatter: Record<string, unknown>): string[] {\n  const raw = frontmatter.aliases;\n  if (!Array.isArray(raw)) return [];\n  return raw.filter((entry): entry is string => typeof entry === \"string\");\n}\n\n/**\n * Map the structural `parseStatus` flags from `src/wiki/collect.ts` into\n * stable viewer warnings. Multiple conditions on one page produce\n * multiple warnings; the order here is the order they appear on the\n * page's `warnings[]`.\n */\nfunction warningsFromParseStatus(page: RawWikiPage): ViewerWarning[] {\n  const warnings: ViewerWarning[] = [];\n  if (!page.parseStatus.hasFrontmatterBlock) {\n    warnings.push({\n      code: \"missing_frontmatter\",\n      message: `Page \"${page.slug}\" has no frontmatter block.`,\n    });\n  } else if (page.parseStatus.malformedFrontmatter) {\n    warnings.push({\n      code: \"malformed_frontmatter\",\n      message: `Page \"${page.slug}\" has malformed YAML frontmatter.`,\n    });\n  }\n  if (!page.parseStatus.hasTitle) {\n    warnings.push({\n      code: \"missing_title\",\n      message: `Page \"${page.slug}\" has no frontmatter title; displaying slug.`,\n    });\n  }\n  return warnings;\n}\n\n","/**\n * Graph data builder for the viewer's `#/graph` route.\n *\n * Converts the flat `ViewerPage[]` list from the startup snapshot into an\n * adjacency representation suitable for D3 force-directed rendering. Called\n * once by `buildViewerSnapshot` — the result is frozen in the snapshot and\n * served directly by `/api/graph` with no per-request computation.\n */\n\nimport type { ViewerPage } from \"./types.js\";\nimport type { GraphData, GraphEdge, GraphNode, PageId } from \"./types.js\";\n\nconst DEFAULT_KIND = \"concept\";\n\n/** Resolve the display kind for a page, defaulting to \"concept\" when absent or non-string. */\nexport function resolvePageKind(frontmatter: Record<string, unknown>): string {\n  return typeof frontmatter.kind === \"string\" && frontmatter.kind.length > 0\n    ? frontmatter.kind\n    : DEFAULT_KIND;\n}\n\n/**\n * Build graph adjacency data from the page list. All outgoing links become\n * edges — including dangling ones whose target has no backing page. Dangling\n * targets appear as ghost nodes with `isDangling: true`. Real-node degree\n * counts only valid edges (dangling out-links do not inflate the source\n * node's out-degree).\n */\nexport function buildGraphData(pages: ViewerPage[]): GraphData {\n  const pageIds = new Set<PageId>(pages.map((p) => p.id));\n  const edges = buildEdges(pages);\n  const ghostDisplayMap = buildGhostDisplayMap(pages);\n  const inDegreeMap = buildInDegreeMap(edges);\n  const realNodes = pages.map((p) => buildNode(p, pageIds, inDegreeMap));\n  const ghostNodes = buildGhostNodes(edges, pageIds, inDegreeMap, ghostDisplayMap);\n  return { nodes: [...realNodes, ...ghostNodes], edges };\n}\n\nfunction buildGhostDisplayMap(pages: ViewerPage[]): Map<PageId, string> {\n  const map = new Map<PageId, string>();\n  for (const page of pages) {\n    for (const { slug, display } of page.danglingLinks ?? []) {\n      const id = ghostId(slug);\n      if (!map.has(id)) map.set(id, display);\n    }\n  }\n  return map;\n}\n\nconst GHOST_DIRECTORY = \"concepts\";\n\n/** Synthesise a stable PageId for an unresolved slug so ghost nodes have a unique key. */\nfunction ghostId(slug: string): PageId {\n  return `${GHOST_DIRECTORY}/${slug}` as PageId;\n}\n\nfunction buildEdges(pages: ViewerPage[]): GraphEdge[] {\n  const edges: GraphEdge[] = [];\n  for (const page of pages) {\n    for (const target of page.outgoingLinks) {\n      edges.push({ source: page.id, target });\n    }\n    for (const { slug } of page.danglingLinks ?? []) {\n      edges.push({ source: page.id, target: ghostId(slug) });\n    }\n  }\n  return edges;\n}\n\nfunction buildGhostNodes(\n  edges: GraphEdge[],\n  pageIds: Set<PageId>,\n  inDegreeMap: Map<PageId, number>,\n  displayMap: Map<PageId, string>,\n): GraphNode[] {\n  const seen = new Set<PageId>();\n  const ghosts: GraphNode[] = [];\n  for (const { target } of edges) {\n    if (pageIds.has(target) || seen.has(target)) continue;\n    seen.add(target);\n    const [directory, ...rest] = target.split(\"/\");\n    const slug = rest.join(\"/\");\n    ghosts.push({\n      id: target,\n      title: displayMap.get(target) ?? slug,\n      slug,\n      directory,\n      kind: \"dangling\",\n      degree: inDegreeMap.get(target) ?? 0,\n      isDangling: true,\n    });\n  }\n  return ghosts;\n}\n\nfunction buildInDegreeMap(edges: GraphEdge[]): Map<PageId, number> {\n  const map = new Map<PageId, number>();\n  for (const edge of edges) {\n    map.set(edge.target, (map.get(edge.target) ?? 0) + 1);\n  }\n  return map;\n}\n\nfunction buildNode(\n  page: ViewerPage,\n  pageIds: Set<PageId>,\n  inDegreeMap: Map<PageId, number>,\n): GraphNode {\n  const outDegree = page.outgoingLinks.filter((t) => pageIds.has(t)).length;\n  const inDegree = inDegreeMap.get(page.id) ?? 0;\n  const kind = resolvePageKind(page.frontmatter);\n  return {\n    id: page.id,\n    title: page.title,\n    slug: page.slug,\n    directory: page.pageDirectory,\n    kind,\n    degree: outDegree + inDegree,\n  };\n}\n","/**\n * Read-only project-state collector for `llmwiki next`.\n *\n * Inspects an llmwiki project root and reports counts, lint cache status,\n * and structural warnings without acquiring locks, mutating disk, or\n * running compile/lint. Designed to be cheap on small projects and to\n * stay cheap on large wikis by using directory mtimes as a stale-lint\n * proxy instead of stat-ing every page.\n *\n * Stale-lint detection is intentionally approximate per the spec:\n * directory-structure changes after the last lint run produce a\n * `lint-cache-stale` warning. Content-only edits may not trigger it on\n * every filesystem; exact lint freshness belongs to `llmwiki lint`.\n *\n * Candidate reads are race-tolerant: this collector delegates to\n * `countCandidates`, which skips malformed/partial candidate JSON the\n * same way `review list` does.\n */\n\nimport { stat, readdir, readFile } from \"fs/promises\";\nimport path from \"path\";\nimport {\n  SOURCES_DIR,\n  CONCEPTS_DIR,\n  QUERIES_DIR,\n  LLMWIKI_DIR,\n  LAST_LINT_FILE,\n  INDEX_FILE,\n} from \"../utils/constants.js\";\nimport { countCandidates } from \"../compiler/candidates.js\";\nimport { LINT_CACHE_TIMESTAMP_PATTERN } from \"../linter/cache.js\";\nimport type { LintCacheEntry } from \"../linter/cache.js\";\nimport { readStateClassified } from \"../utils/state.js\";\n\n/** Markdown extension treated as a wiki page for counting purposes. */\nconst MARKDOWN_EXT = \".md\";\n\n/** Warning codes the v1 collector may emit. Pinned by tests. */\ntype ProjectStateWarningCode =\n  | \"lint-cache-stale\"\n  | \"lint-cache-unparseable\"\n  | \"freshness-cache-stale\"\n  | \"index-missing\"\n  | \"sources-not-compiled\"\n  | \"pending-candidates\"\n  | \"project-unreadable\"\n  | \"state-unreadable\"\n  | \"stale-pages\";\n\n/** One structural warning surfaced alongside the primary state. */\nexport interface ProjectStateWarning {\n  code: ProjectStateWarningCode;\n  message: string;\n}\n\n/** Three-state lint-cache shape per the JSON contract. */\ninterface LintCacheStatus {\n  /** True when a cache file exists on disk, even if it failed to parse. */\n  present: boolean;\n  /** Parsed cache entry; null when no file exists OR file failed to parse. */\n  entry: LintCacheEntry | null;\n}\n\n/** Full project-state snapshot consumed by `recommendNextAction` and renderers. */\nexport interface ProjectState {\n  root: string;\n  hasSourcesDir: boolean;\n  hasWikiDir: boolean;\n  hasInternalDir: boolean;\n  sourceCount: number;\n  conceptCount: number;\n  queryCount: number;\n  pendingCandidates: number;\n  hasIndex: boolean;\n  lint: LintCacheStatus;\n  latestWikiMtimeMs: number | null;\n  latestSourceMtimeMs: number | null;\n  warnings: ProjectStateWarning[];\n}\n\n/**\n * Collect a full ProjectState snapshot for `root`. Never throws on\n * expected absent-file paths — those become `false`/`0`/`null` fields.\n * Returns a `project-unreadable` warning when the root itself cannot be\n * stat-ed; callers escalate that to the `broken-project` primary state.\n */\nexport async function collectProjectState(root: string): Promise<ProjectState> {\n  const rootReadable = await isDirectory(root);\n  if (!rootReadable) return brokenProjectState(root);\n  const dirs = await collectDirPresence(root);\n  const counts = await collectPageCounts(root, dirs);\n  const lint = await collectLintCacheStatus(root);\n  const mtimes = await collectMtimes(root, dirs);\n  // Read-only; never writes a .bak file — safe for the cheap orientation command.\n  const stateStatus = (await readStateClassified(root)).status;\n  return assembleState({ root, dirs, counts, lint, mtimes, stateStatus });\n}\n\n/** State returned when `root` itself cannot be inspected. */\nfunction brokenProjectState(root: string): ProjectState {\n  return {\n    root,\n    hasSourcesDir: false,\n    hasWikiDir: false,\n    hasInternalDir: false,\n    sourceCount: 0,\n    conceptCount: 0,\n    queryCount: 0,\n    pendingCandidates: 0,\n    hasIndex: false,\n    lint: { present: false, entry: null },\n    latestWikiMtimeMs: null,\n    latestSourceMtimeMs: null,\n    warnings: [\n      {\n        code: \"project-unreadable\",\n        message: `Project root is unreadable or could not be inspected: ${root}`,\n      },\n    ],\n  };\n}\n\n/** Cheap presence probes for the three structural directories the recommender keys on. */\ninterface DirPresence {\n  hasSourcesDir: boolean;\n  hasWikiDir: boolean;\n  hasInternalDir: boolean;\n}\n\n/** Raw page counts surfaced into ProjectState; computed in one pass to keep collectProjectState short. */\ninterface PageCounts {\n  sourceCount: number;\n  conceptCount: number;\n  queryCount: number;\n  pendingCandidates: number;\n  hasIndex: boolean;\n}\n\n/** Mtime proxies used for the cheap stale-lint approximation. */\ninterface MtimePair {\n  latestWikiMtimeMs: number | null;\n  latestSourceMtimeMs: number | null;\n}\n\n/** Probe the three structural directories without listing their contents. */\nasync function collectDirPresence(root: string): Promise<DirPresence> {\n  const [hasSourcesDir, hasWikiDir, hasInternalDir] = await Promise.all([\n    isDirectory(path.join(root, SOURCES_DIR)),\n    isDirectory(path.join(root, \"wiki\")),\n    isDirectory(path.join(root, LLMWIKI_DIR)),\n  ]);\n  return { hasSourcesDir, hasWikiDir, hasInternalDir };\n}\n\n/** Compute page counts plus the wiki/index.md presence flag. */\nasync function collectPageCounts(root: string, dirs: DirPresence): Promise<PageCounts> {\n  const [sourceCount, conceptCount, queryCount, pendingCandidates, hasIndex] = await Promise.all([\n    dirs.hasSourcesDir ? countMarkdownFiles(path.join(root, SOURCES_DIR)) : 0,\n    dirs.hasWikiDir ? countMarkdownFiles(path.join(root, CONCEPTS_DIR)) : 0,\n    dirs.hasWikiDir ? countMarkdownFiles(path.join(root, QUERIES_DIR)) : 0,\n    dirs.hasInternalDir ? safeCountCandidates(root) : 0,\n    dirs.hasWikiDir ? isFile(path.join(root, INDEX_FILE)) : false,\n  ]);\n  return { sourceCount, conceptCount, queryCount, pendingCandidates, hasIndex };\n}\n\n/** Read directory mtimes only when the directories exist; absent dirs report null. */\nasync function collectMtimes(root: string, dirs: DirPresence): Promise<MtimePair> {\n  const [latestWikiMtimeMs, latestSourceMtimeMs] = await Promise.all([\n    dirs.hasWikiDir ? safeMtime(path.join(root, \"wiki\")) : Promise.resolve(null),\n    dirs.hasSourcesDir ? safeMtime(path.join(root, SOURCES_DIR)) : Promise.resolve(null),\n  ]);\n  return { latestWikiMtimeMs, latestSourceMtimeMs };\n}\n\n/** Read and validate the lint cache, distinguishing missing from corrupt. */\nasync function collectLintCacheStatus(root: string): Promise<LintCacheStatus> {\n  const cachePath = path.join(root, LAST_LINT_FILE);\n  const exists = await isFile(cachePath);\n  if (!exists) return { present: false, entry: null };\n  const entry = await readLintCacheEntry(cachePath);\n  return { present: true, entry };\n}\n\n/** Strict parse + validate, returning null for any unreadable/corrupt cache file. */\nasync function readLintCacheEntry(cachePath: string): Promise<LintCacheEntry | null> {\n  let raw: string;\n  try {\n    raw = await readFile(cachePath, \"utf-8\");\n  } catch {\n    return null;\n  }\n  try {\n    const parsed = JSON.parse(raw) as unknown;\n    return validateCacheShape(parsed);\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Validate the lint cache JSON shape, carrying the optional `freshness` field\n * through when it is present and well-formed. Returns null for any missing or\n * corrupt field in the required subset ({@link LintCacheEntry}).\n */\nfunction validateCacheShape(value: unknown): LintCacheEntry | null {\n  if (typeof value !== \"object\" || value === null) return null;\n  const candidate = value as Record<string, unknown>;\n  const { warnings, errors, at, freshness } = candidate;\n  if (!isNonNegativeInteger(warnings)) return null;\n  if (!isNonNegativeInteger(errors)) return null;\n  if (typeof at !== \"string\" || !LINT_CACHE_TIMESTAMP_PATTERN.test(at)) return null;\n  const entry: LintCacheEntry = { warnings, errors, at };\n  // Intentionally lenient (diverges from cache.ts:isValidEntry): a malformed\n  // `freshness` sub-field is silently dropped rather than rejecting the whole\n  // entry, so `next` still surfaces valid lint counts. Do not \"align\" the two.\n  if (isValidFreshnessShape(freshness)) entry.freshness = freshness;\n  return entry;\n}\n\n/** True when `value` is a well-formed freshness sub-object. */\nfunction isValidFreshnessShape(\n  value: unknown,\n): value is { stalePages: number; orphanedPages: number } {\n  if (typeof value !== \"object\" || value === null) return false;\n  const c = value as Record<string, unknown>;\n  return isNonNegativeInteger(c.stalePages) && isNonNegativeInteger(c.orphanedPages);\n}\n\n/** True for finite, non-negative integers. NaN and Infinity fail Number.isInteger. */\nfunction isNonNegativeInteger(value: unknown): value is number {\n  return typeof value === \"number\" && Number.isInteger(value) && value >= 0;\n}\n\n/** Inputs to {@link assembleState}, grouped to keep the function's arity within limits. */\ninterface AssembleStateInput {\n  root: string;\n  dirs: DirPresence;\n  counts: PageCounts;\n  lint: LintCacheStatus;\n  mtimes: MtimePair;\n  stateStatus: \"ok\" | \"missing\" | \"corrupt\";\n}\n\n/** Combine the per-section reads into the final ProjectState + warning list. */\nfunction assembleState(input: AssembleStateInput): ProjectState {\n  const { root, dirs, counts, lint, mtimes, stateStatus } = input;\n  const warnings = buildWarnings({ dirs, counts, lint, mtimes, stateStatus });\n  return { root, ...dirs, ...counts, lint, ...mtimes, warnings };\n}\n\n/** Inputs for warning derivation; passed as a record to keep argument lists short. */\ninterface WarningInput {\n  dirs: DirPresence;\n  counts: PageCounts;\n  lint: LintCacheStatus;\n  mtimes: MtimePair;\n  stateStatus: \"ok\" | \"missing\" | \"corrupt\";\n}\n\n/** Derive every structural warning from the already-collected state slices. */\nfunction buildWarnings(input: WarningInput): ProjectStateWarning[] {\n  const warnings: ProjectStateWarning[] = [];\n  appendLintWarnings(warnings, input.lint, input.mtimes.latestWikiMtimeMs);\n  appendStructuralWarnings(warnings, input.dirs, input.counts);\n  appendFreshnessWarnings(warnings, input.lint, input.stateStatus, input.mtimes.latestSourceMtimeMs);\n  return warnings;\n}\n\n/** Lint-cache warnings: unparseable file or stale-vs-wiki-mtime. */\nfunction appendLintWarnings(\n  warnings: ProjectStateWarning[],\n  lint: LintCacheStatus,\n  latestWikiMtimeMs: number | null,\n): void {\n  if (lint.present && lint.entry === null) {\n    warnings.push({\n      code: \"lint-cache-unparseable\",\n      message: \"Lint cache file exists but could not be parsed. Re-run `llmwiki lint`.\",\n    });\n    return;\n  }\n  if (lint.entry && isLintCacheStale(lint.entry, latestWikiMtimeMs)) {\n    warnings.push({\n      code: \"lint-cache-stale\",\n      message: \"Lint cache is older than the wiki directory; pages were added or removed since the last lint.\",\n    });\n  }\n}\n\n/** Structural warnings: missing index, pending candidates, uncompiled sources. */\nfunction appendStructuralWarnings(\n  warnings: ProjectStateWarning[],\n  dirs: DirPresence,\n  counts: PageCounts,\n): void {\n  const hasPages = counts.conceptCount > 0 || counts.queryCount > 0;\n  if (hasPages && !counts.hasIndex) {\n    warnings.push({\n      code: \"index-missing\",\n      message: \"wiki/index.md is missing even though pages exist.\",\n    });\n  }\n  if (counts.pendingCandidates > 0) {\n    warnings.push({\n      code: \"pending-candidates\",\n      message: `${counts.pendingCandidates} generated candidate${counts.pendingCandidates === 1 ? \"\" : \"s\"} waiting for review.`,\n    });\n  }\n  if (dirs.hasSourcesDir && counts.sourceCount > 0 && !hasPages) {\n    warnings.push({\n      code: \"sources-not-compiled\",\n      message: \"Sources exist but no wiki pages were found. Run `llmwiki compile`.\",\n    });\n  }\n}\n\n/**\n * Freshness warnings: corrupt state.json (fail-loud, not silent), stale/orphaned\n * page counts from the lint cache, and a heuristic freshness-cache-stale warning\n * when sources/ changed after the last lint.\n *\n * Missing state stays quiet — it is normal before the first compile.\n * Only corrupt state warns because it silently zeros all findings.\n */\nfunction appendFreshnessWarnings(\n  warnings: ProjectStateWarning[],\n  lint: LintCacheStatus,\n  stateStatus: \"ok\" | \"missing\" | \"corrupt\",\n  latestSourceMtimeMs: number | null,\n): void {\n  if (stateStatus === \"corrupt\") {\n    warnings.push({\n      code: \"state-unreadable\",\n      message:\n        \".llmwiki/state.json is corrupt — run `llmwiki compile` to rebuild it (freshness figures shown are from the last lint and may be stale).\",\n    });\n  }\n  const f = lint.entry?.freshness;\n  if (f && (f.stalePages > 0 || f.orphanedPages > 0)) {\n    warnings.push({\n      code: \"stale-pages\",\n      message: `${f.stalePages} stale, ${f.orphanedPages} orphaned page(s) as of the last lint — run \\`llmwiki compile\\` to refresh.`,\n    });\n  }\n  if (lint.entry && isFreshnessCacheStale(lint.entry, latestSourceMtimeMs)) {\n    warnings.push({\n      code: \"freshness-cache-stale\",\n      message:\n        \"sources/ changed since the last lint — freshness counts may be out of date; run `llmwiki lint` to refresh.\",\n    });\n  }\n}\n\n/**\n * Heuristic: the sources/ directory mtime is newer than the last lint run.\n * Catches added/removed source files; may NOT detect in-place content edits on\n * all filesystems (same limitation as the wiki-mtime lint-cache-stale check).\n */\nfunction isFreshnessCacheStale(entry: LintCacheEntry, latestSourceMtimeMs: number | null): boolean {\n  if (latestSourceMtimeMs === null) return false;\n  const lintMs = Date.parse(entry.at);\n  if (Number.isNaN(lintMs)) return false;\n  return latestSourceMtimeMs > lintMs;\n}\n\n/** Cheap structural staleness: last-lint timestamp older than wiki dir mtime. */\nfunction isLintCacheStale(entry: LintCacheEntry, latestWikiMtimeMs: number | null): boolean {\n  if (latestWikiMtimeMs === null) return false;\n  const lintMs = Date.parse(entry.at);\n  if (Number.isNaN(lintMs)) return false;\n  return latestWikiMtimeMs > lintMs;\n}\n\n/** True when `target` is a directory; false for missing paths or any other type. */\nasync function isDirectory(target: string): Promise<boolean> {\n  try {\n    const stats = await stat(target);\n    return stats.isDirectory();\n  } catch {\n    return false;\n  }\n}\n\n/** True when `target` is a regular file; false for missing paths or directories. */\nasync function isFile(target: string): Promise<boolean> {\n  try {\n    const stats = await stat(target);\n    return stats.isFile();\n  } catch {\n    return false;\n  }\n}\n\n/** Directory mtime in ms epoch, or null when the directory cannot be stat-ed. */\nasync function safeMtime(target: string): Promise<number | null> {\n  try {\n    const stats = await stat(target);\n    return stats.mtimeMs;\n  } catch {\n    return null;\n  }\n}\n\n/** Count `.md` files in a directory; 0 for missing dirs or any other error. */\nasync function countMarkdownFiles(dir: string): Promise<number> {\n  try {\n    const entries = await readdir(dir, { withFileTypes: true });\n    let count = 0;\n    for (const entry of entries) {\n      if (entry.isFile() && entry.name.endsWith(MARKDOWN_EXT)) count += 1;\n    }\n    return count;\n  } catch {\n    return 0;\n  }\n}\n\n/** Race-tolerant candidate count; defers to `countCandidates` and swallows IO errors. */\nasync function safeCountCandidates(root: string): Promise<number> {\n  try {\n    return await countCandidates(root);\n  } catch {\n    return 0;\n  }\n}\n","/**\n * Persistent cache of the most recent `llmwiki lint` run.\n *\n * Written by the lint command after a completed run, before any non-zero exit\n * for lint findings, so the cache always reflects the run the user just saw.\n * Crashed or partial runs leave the prior cache untouched.\n *\n * Consumers (e.g., the upcoming viewer's /api/health endpoint) read the cache\n * to surface lint counts without re-running lint per request. A missing or\n * malformed cache reads as null, which means \"lint has not been run yet.\"\n */\n\nimport { mkdir, readFile } from \"fs/promises\";\nimport path from \"path\";\nimport { atomicWrite } from \"../utils/markdown.js\";\nimport { LLMWIKI_DIR, LAST_LINT_FILE } from \"../utils/constants.js\";\nimport type { LintSummary } from \"./types.js\";\n\n/** Per-rule freshness counts, derived from the lint results. Optional so a pre-upgrade cache still parses. */\nexport interface LintFreshnessCounts {\n  stalePages: number;\n  orphanedPages: number;\n}\n\n/** One persisted lint summary. Shape is part of the public viewer-cache contract. */\nexport interface LintCacheEntry {\n  warnings: number;\n  errors: number;\n  /** ISO-8601 timestamp of the run that produced these counts. */\n  at: string;\n  /** Stale/orphaned page counts from the freshness lint rule. Absent on pre-0.9 caches. */\n  freshness?: LintFreshnessCounts;\n}\n\n/**\n * The exact ISO-8601 shape `writeLintCache` produces and `readLintCache` accepts.\n * Exported so tests can assert against the same regex the validator enforces and\n * never drift from the documented contract.\n */\nexport const LINT_CACHE_TIMESTAMP_PATTERN = /^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}\\.\\d{3}Z$/;\n\n/** Count results emitted by a given lint rule. */\nfunction countByRule(results: LintSummary[\"results\"], rule: string): number {\n  return results.filter((r) => r.rule === rule).length;\n}\n\n/**\n * Persist a lint summary to `.llmwiki/last-lint.json` after a completed run.\n * Creates the `.llmwiki/` directory if missing. Overwrites any prior entry so\n * the cache reflects the most recent run, including zero-issue runs.\n */\nexport async function writeLintCache(root: string, summary: LintSummary): Promise<void> {\n  await mkdir(path.join(root, LLMWIKI_DIR), { recursive: true });\n  const entry: LintCacheEntry = {\n    warnings: summary.warnings,\n    errors: summary.errors,\n    at: new Date().toISOString(),\n    freshness: {\n      stalePages: countByRule(summary.results, \"stale-page\"),\n      orphanedPages: countByRule(summary.results, \"orphaned-page\"),\n    },\n  };\n  await atomicWrite(path.join(root, LAST_LINT_FILE), `${JSON.stringify(entry, null, 2)}\\n`);\n}\n\n/**\n * Read the cached lint summary, returning null for missing or malformed files.\n * Validation is strict: every field must have its expected type, otherwise the\n * cache is treated as absent so callers do not surface garbage counts.\n */\nexport async function readLintCache(root: string): Promise<LintCacheEntry | null> {\n  let raw: string;\n  try {\n    raw = await readFile(path.join(root, LAST_LINT_FILE), \"utf-8\");\n  } catch {\n    return null;\n  }\n  let parsed: unknown;\n  try {\n    parsed = JSON.parse(raw);\n  } catch {\n    return null;\n  }\n  if (!isValidEntry(parsed)) return null;\n  return {\n    warnings: parsed.warnings,\n    errors: parsed.errors,\n    at: parsed.at,\n    ...(parsed.freshness !== undefined ? { freshness: parsed.freshness } : {}),\n  };\n}\n\n/** True for finite non-negative integers, including zero. NaN and Infinity fail Number.isInteger. */\nfunction isNonNegativeInteger(value: unknown): value is number {\n  return typeof value === \"number\" && Number.isInteger(value) && value >= 0;\n}\n\n/** Validates the optional freshness sub-object; rejects if present but malformed. */\nfunction isValidFreshness(value: unknown): value is LintFreshnessCounts {\n  if (typeof value !== \"object\" || value === null) return false;\n  const c = value as Record<string, unknown>;\n  return isNonNegativeInteger(c.stalePages) && isNonNegativeInteger(c.orphanedPages);\n}\n\n/**\n * Strict type guard for the persisted cache entry.\n *\n * Counts must be finite non-negative integers (the writer only ever persists\n * `LintSummary` severity counts, which originate from a length on an array, so\n * anything else means the file was hand-edited or corrupted). The timestamp\n * must match the exact ISO-8601 shape the writer produces, otherwise downstream\n * consumers risk surfacing values like \"2026-01-01\" as full timestamps.\n * The `freshness` field is optional — pre-upgrade caches omitting it still parse.\n */\nfunction isValidEntry(value: unknown): value is LintCacheEntry {\n  if (typeof value !== \"object\" || value === null) return false;\n  const candidate = value as Record<string, unknown>;\n  if (\n    !isNonNegativeInteger(candidate.warnings) ||\n    !isNonNegativeInteger(candidate.errors) ||\n    typeof candidate.at !== \"string\" ||\n    !LINT_CACHE_TIMESTAMP_PATTERN.test(candidate.at)\n  ) {\n    return false;\n  }\n  if (candidate.freshness !== undefined && !isValidFreshness(candidate.freshness)) return false;\n  return true;\n}\n","/**\n * Pure recommendation rules for `llmwiki next`.\n *\n * Classifies a {@link ProjectState} snapshot into exactly one of seven\n * primary states and produces a primary {@link RecommendedAction} plus\n * the per-state `otherActions` table from the implementation plan.\n *\n * Actions with user-supplied input (a source path, a question, a\n * candidate id) are templates: the display `command` carries a\n * `<placeholder>` and `executable.placeholders` lists the slots. Agents\n * must populate placeholders themselves; the contract never returns a\n * shell-ready command line.\n */\n\nimport type { ProjectState } from \"./state.js\";\n\n/** Primary state enum surfaced as `state` in the JSON envelope. */\nexport type ProjectStateKind =\n  | \"fresh\"\n  | \"sources-only\"\n  | \"review-pending\"\n  | \"lint-attention\"\n  | \"wiki-ready\"\n  | \"empty-wiki\"\n  | \"broken-project\";\n\n/** Single recommended action; `command` is for display, `executable` is for agents. */\nexport interface RecommendedAction {\n  command: string | null;\n  reason: string;\n  executable: ExecutableSpec | null;\n}\n\n/** Structured form of an executable command. Placeholders are slot names, not literals. */\ninterface ExecutableSpec {\n  binary: \"llmwiki\";\n  args: string[];\n  placeholders?: string[];\n}\n\n/** Full recommendation envelope returned to the renderer. */\nexport interface Recommendation {\n  state: ProjectStateKind;\n  recommended: RecommendedAction;\n  otherActions: RecommendedAction[];\n}\n\n/**\n * Classify a ProjectState and produce its primary + secondary actions.\n * Precedence (top wins): broken-project, fresh, sources-only,\n * review-pending, lint-attention, wiki-ready, empty-wiki.\n */\nexport function recommendNextAction(state: ProjectState): Recommendation {\n  const kind = classifyState(state);\n  return { state: kind, recommended: primaryAction(kind), otherActions: otherActionsFor(kind) };\n}\n\n/** Apply the precedence rules from the spec to choose the primary state kind. */\nfunction classifyState(state: ProjectState): ProjectStateKind {\n  if (isBrokenProject(state)) return \"broken-project\";\n  if (isSourcesOnly(state)) return \"sources-only\";\n  if (state.pendingCandidates > 0) return \"review-pending\";\n  if (hasLintErrors(state)) return \"lint-attention\";\n  if (hasWikiPages(state)) return \"wiki-ready\";\n  if (isEmptyWiki(state)) return \"empty-wiki\";\n  return \"fresh\";\n}\n\n/** True when the collector flagged the root as unreadable. */\nfunction isBrokenProject(state: ProjectState): boolean {\n  return state.warnings.some((w) => w.code === \"project-unreadable\");\n}\n\n/**\n * `empty-wiki` requires `wiki/` to actually exist with zero pages. The\n * spec wording is \"wiki/ exists but page count is zero\", and the human\n * renderer says so — we must not surface that line when wiki/ is missing.\n */\nfunction isEmptyWiki(state: ProjectState): boolean {\n  return state.hasWikiDir && !hasWikiPages(state);\n}\n\n/** Sources exist but no concept or query pages have been compiled yet. */\nfunction isSourcesOnly(state: ProjectState): boolean {\n  return state.sourceCount > 0 && !hasWikiPages(state);\n}\n\n/** True when the lint cache parsed and reports at least one error. */\nfunction hasLintErrors(state: ProjectState): boolean {\n  return state.lint.entry !== null && state.lint.entry.errors > 0;\n}\n\n/** True when the wiki carries any concept or query page. */\nfunction hasWikiPages(state: ProjectState): boolean {\n  return state.conceptCount > 0 || state.queryCount > 0;\n}\n\n/** Map a state kind to its primary recommended action. */\nfunction primaryAction(kind: ProjectStateKind): RecommendedAction {\n  return PRIMARY_ACTIONS[kind];\n}\n\n/** Map a state kind to its `otherActions` list. */\nfunction otherActionsFor(kind: ProjectStateKind): RecommendedAction[] {\n  return OTHER_ACTIONS[kind].map((a) => ({ ...a }));\n}\n\n/** Template action: `llmwiki quickstart <source>` with a `source` placeholder. */\nconst QUICKSTART_ACTION: RecommendedAction = {\n  command: \"llmwiki quickstart <source>\",\n  reason: \"Ingest a source and compile a wiki in one step.\",\n  executable: { binary: \"llmwiki\", args: [\"quickstart\"], placeholders: [\"source\"] },\n};\n\n/** Template action: `llmwiki ingest <source>`. */\nconst INGEST_ACTION: RecommendedAction = {\n  command: \"llmwiki ingest <source>\",\n  reason: \"Add sources manually before compiling.\",\n  executable: { binary: \"llmwiki\", args: [\"ingest\"], placeholders: [\"source\"] },\n};\n\n/** Bare action: `llmwiki compile`. */\nconst COMPILE_ACTION: RecommendedAction = {\n  command: \"llmwiki compile\",\n  reason: \"Compile sources/ into wiki pages.\",\n  executable: { binary: \"llmwiki\", args: [\"compile\"] },\n};\n\n/** Bare action: `llmwiki review list`. */\nconst REVIEW_LIST_ACTION: RecommendedAction = {\n  command: \"llmwiki review list\",\n  reason: \"List pending candidate pages.\",\n  executable: { binary: \"llmwiki\", args: [\"review\", \"list\"] },\n};\n\n/** Template action: `llmwiki review approve <id>`. */\nconst REVIEW_APPROVE_ACTION: RecommendedAction = {\n  command: \"llmwiki review approve <id>\",\n  reason: \"Approve a candidate after inspecting it with `llmwiki review show <id>`.\",\n  executable: { binary: \"llmwiki\", args: [\"review\", \"approve\"], placeholders: [\"id\"] },\n};\n\n/** Bare action: `llmwiki lint`. */\nconst LINT_ACTION: RecommendedAction = {\n  command: \"llmwiki lint\",\n  reason: \"Re-run lint to inspect outstanding errors.\",\n  executable: { binary: \"llmwiki\", args: [\"lint\"] },\n};\n\n/** Bare action: `llmwiki view --open`. */\nconst VIEW_OPEN_ACTION: RecommendedAction = {\n  command: \"llmwiki view --open\",\n  reason: \"Browse the compiled wiki in the local viewer.\",\n  executable: { binary: \"llmwiki\", args: [\"view\", \"--open\"] },\n};\n\n/** Template action: `llmwiki query \"<question>\"`. */\nconst QUERY_ACTION: RecommendedAction = {\n  command: 'llmwiki query \"<question>\"',\n  reason: \"Ask a natural-language question against the compiled wiki.\",\n  executable: { binary: \"llmwiki\", args: [\"query\"], placeholders: [\"question\"] },\n};\n\n/** Sentinel for the broken-project state: no command, no executable. */\nconst BROKEN_PROJECT_ACTION: RecommendedAction = {\n  command: null,\n  reason: \"Project root is unreadable or could not be inspected.\",\n  executable: null,\n};\n\n/** Primary recommendation for each state kind. */\nconst PRIMARY_ACTIONS: Record<ProjectStateKind, RecommendedAction> = {\n  \"broken-project\": BROKEN_PROJECT_ACTION,\n  fresh: { ...QUICKSTART_ACTION, reason: \"No sources or wiki pages were found.\" },\n  \"sources-only\": { ...COMPILE_ACTION, reason: \"Sources exist but no wiki pages have been compiled.\" },\n  \"review-pending\": { ...REVIEW_LIST_ACTION, reason: \"Generated candidates are waiting for review.\" },\n  \"lint-attention\": { ...LINT_ACTION, reason: \"Lint has reported errors; rerun lint to inspect them.\" },\n  \"wiki-ready\": { ...VIEW_OPEN_ACTION, reason: \"Wiki pages are ready to browse.\" },\n  \"empty-wiki\": {\n    ...COMPILE_ACTION,\n    reason: \"wiki/ exists but is empty; run compile or add sources first.\",\n  },\n};\n\n/** Per-state otherActions table from the implementation plan (Slice 1 scope). */\nconst OTHER_ACTIONS: Record<ProjectStateKind, RecommendedAction[]> = {\n  fresh: [INGEST_ACTION, QUICKSTART_ACTION],\n  \"sources-only\": [COMPILE_ACTION, QUICKSTART_ACTION],\n  \"empty-wiki\": [COMPILE_ACTION, INGEST_ACTION],\n  \"review-pending\": [REVIEW_LIST_ACTION, REVIEW_APPROVE_ACTION],\n  \"lint-attention\": [LINT_ACTION, VIEW_OPEN_ACTION],\n  \"wiki-ready\": [VIEW_OPEN_ACTION, QUERY_ACTION],\n  \"broken-project\": [],\n};\n","/**\n * Server-side title/body search over the startup `ViewerSnapshot`.\n *\n * V1 semantics (spec §Slice 5 \"Search semantics\"):\n *   - case-insensitive\n *   - whitespace-tokenized\n *   - multi-token AND: every token must appear in either title or body\n *   - title matches rank before body matches\n *   - 200-char query cap, 50-result cap\n *   - concept and query pages only — `wiki/index.md` is excluded by\n *     construction (it never lives in `snapshot.pages`)\n *   - no fuzzy matching, stemming, regex, or client-side search\n *\n * The search reads from the snapshot exclusively — no per-request disk\n * I/O — so it inherits the same \"frozen at startup, restart to refresh\"\n * lifecycle as the rest of the viewer's API.\n */\n\nimport type { PageId, ViewerPage, ViewerSnapshot } from \"./types.js\";\nimport type { PageDirectory } from \"../export/types.js\";\n\nconst MAX_QUERY_LENGTH = 200;\nconst MAX_RESULTS = 50;\nconst SNIPPET_RADIUS = 60;\nconst SNIPPET_ELLIPSIS = \"…\";\n\n/** Where the query matched in a result page. */\ntype SearchMatch = \"title\" | \"body\";\n\n/** One row in the `/api/search` response. */\ninterface SearchResult {\n  id: PageId;\n  pageDirectory: PageDirectory;\n  title: string;\n  snippet: string;\n  matchedIn: SearchMatch;\n}\n\n/**\n * Run a search over the snapshot and return the results envelope. Pure\n * over `(snapshot, rawQuery)` — the same inputs always produce the same\n * output, which lets the route handler stay a one-line adapter.\n */\nexport function searchPages(\n  snapshot: ViewerSnapshot,\n  rawQuery: string,\n): { results: SearchResult[] } {\n  const tokens = tokenizeQuery(rawQuery);\n  if (tokens.length === 0) return { results: [] };\n  const matches = collectMatches(snapshot.pages, tokens);\n  matches.sort(compareResults);\n  return { results: matches.slice(0, MAX_RESULTS) };\n}\n\n/**\n * Trim, lowercase, cap at 200 characters, then split on any run of\n * whitespace. Empty tokens are dropped so trailing/leading spaces or\n * a runaway over-cap query still produce sensible tokens.\n */\nfunction tokenizeQuery(rawQuery: string): string[] {\n  if (typeof rawQuery !== \"string\") return [];\n  const trimmed = rawQuery.trim();\n  if (trimmed.length === 0) return [];\n  const capped = trimmed.slice(0, MAX_QUERY_LENGTH).toLowerCase();\n  return capped.split(/\\s+/).filter((t) => t.length > 0);\n}\n\n/** Iterate the snapshot pages and emit one result per match. */\nfunction collectMatches(pages: ReadonlyArray<ViewerPage>, tokens: string[]): SearchResult[] {\n  const matches: SearchResult[] = [];\n  for (const page of pages) {\n    const result = matchPage(page, tokens);\n    if (result) matches.push(result);\n  }\n  return matches;\n}\n\n/**\n * Decide whether `page` matches `tokens`. Per spec §Slice 5 Search\n * Semantics: \"every token must appear in title or body\" — each token\n * individually must appear in the title-or-body union. Classification\n * (`matchedIn`) is \"title\" only when every token is found in the title;\n * any token that only matched the body downgrades the page to a body\n * hit, which then ranks below title hits.\n */\nfunction matchPage(page: ViewerPage, tokens: string[]): SearchResult | null {\n  const titleLower = page.title.toLowerCase();\n  const bodyLower = page.body.toLowerCase();\n  for (const token of tokens) {\n    if (!titleLower.includes(token) && !bodyLower.includes(token)) return null;\n  }\n  const allInTitle = tokens.every((t) => titleLower.includes(t));\n  if (allInTitle) return rowFromPage(page, page.title, \"title\");\n  const snippet = buildBodySnippet(page.body, bodyLower, tokens);\n  return rowFromPage(page, snippet, \"body\");\n}\n\n/** Assemble a SearchResult from a page + computed snippet. */\nfunction rowFromPage(page: ViewerPage, snippet: string, matchedIn: SearchMatch): SearchResult {\n  return {\n    id: page.id,\n    pageDirectory: page.pageDirectory,\n    title: page.title,\n    snippet,\n    matchedIn,\n  };\n}\n\n/**\n * Extract ±SNIPPET_RADIUS chars around the earliest token match in the\n * body. Newlines are flattened to single spaces so the snippet renders\n * inline in the results panel. `…` is prepended/appended when the\n * window was truncated at either end.\n */\nfunction buildBodySnippet(body: string, bodyLower: string, tokens: string[]): string {\n  const matchPos = earliestTokenPosition(bodyLower, tokens);\n  const start = Math.max(0, matchPos - SNIPPET_RADIUS);\n  const end = Math.min(body.length, matchPos + SNIPPET_RADIUS);\n  const cleaned = stripInlineMarkdownNoise(body.slice(start, end))\n    .replace(/\\s+/g, \" \")\n    .trim();\n  const prefix = start > 0 ? SNIPPET_ELLIPSIS : \"\";\n  const suffix = end < body.length ? SNIPPET_ELLIPSIS : \"\";\n  return `${prefix}${cleaned}${suffix}`;\n}\n\n/**\n * Strip common inline-markdown markers from a snippet so the search\n * results panel shows readable prose rather than `**keyword**` and\n * `[label](url)` noise. Intentionally narrow: only handles the\n * inline-marker forms a reader would mistake for typos. Block-level\n * markers (`#` headings, `>` blockquotes) are left alone — they sit at\n * the start of a line and rarely land inside a ±60-char window.\n */\nfunction stripInlineMarkdownNoise(text: string): string {\n  return text\n    .replace(/!\\[([^\\]]*)\\]\\([^)]*\\)/g, \"$1\")\n    .replace(/\\[([^\\]]+)\\]\\([^)]*\\)/g, \"$1\")\n    .replace(/\\[\\[([^\\]|\\n]+)\\|([^\\]\\n]+)\\]\\]/g, \"$2\")\n    .replace(/\\[\\[([^\\]\\n]+)\\]\\]/g, \"$1\")\n    .replace(/\\*\\*([^*]+)\\*\\*/g, \"$1\")\n    .replace(/__([^_]+)__/g, \"$1\")\n    .replace(/(?<!\\w)\\*([^*\\n]+)\\*(?!\\w)/g, \"$1\")\n    .replace(/(?<!\\w)_([^_\\n]+)_(?!\\w)/g, \"$1\")\n    .replace(/`([^`\\n]+)`/g, \"$1\")\n    .replace(/~~([^~\\n]+)~~/g, \"$1\");\n}\n\n/** Earliest index where any token first appears in the body. */\nfunction earliestTokenPosition(bodyLower: string, tokens: string[]): number {\n  let earliest = bodyLower.length;\n  for (const token of tokens) {\n    const idx = bodyLower.indexOf(token);\n    if (idx >= 0 && idx < earliest) earliest = idx;\n  }\n  return earliest;\n}\n\n/**\n * Title hits sort before body hits. Within the same `matchedIn` bucket\n * the order is stable by title (alphabetical, locale-aware) so the\n * result list does not shift between requests against the same snapshot.\n */\nfunction compareResults(a: SearchResult, b: SearchResult): number {\n  if (a.matchedIn !== b.matchedIn) {\n    return a.matchedIn === \"title\" ? -1 : 1;\n  }\n  return a.title.localeCompare(b.title);\n}\n","/**\n * Provenance helpers for `llmwiki context`.\n *\n * Slice 4 ships two related pieces of work:\n *   1. Flatten `ViewerPage.citations` (`ClaimCitation[]`, each with one\n *      or more `SourceSpan` entries) into the documented\n *      `ContextPrimary.citations[]` shape: one object per span,\n *      `file`/`start`/`end` lifted from `span.lines` when present,\n *      paragraph-only citations omit `start`/`end`, de-duped by\n *      `(file, start, end)`, preserved in first-seen document order\n *      (plan §Provenance And Source Windows).\n *   2. Materialize bounded `ContextSourceWindow[]` for `--include-sources`\n *      by reading short line ranges out of `sources/`. Path-confined:\n *      traversal, absolute paths, and symlink escapes are rejected.\n *      Only claim-level spans (`lines` populated) become windows;\n *      paragraph-only citations are intentionally skipped because the\n *      caller asked for SPECIFIC line context, not whole files.\n *\n * Citation flattening is the inner contract for `primary[].citations`;\n * source-window materialization is the outer guard rail for\n * `--include-sources` per-pack and per-window caps.\n */\n\nimport { promises as fs } from \"fs\";\nimport path from \"path\";\nimport type { ClaimCitation, SourceSpan } from \"../utils/types.js\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\n\n/** Per-pack ceiling on emitted source windows. */\nexport const MAX_SOURCE_WINDOWS = 20;\n/** Per-window ceiling on lines read out of a source file. */\nexport const MAX_LINES_PER_WINDOW = 30;\n/**\n * Visible ASCII delimiter for {@link citationKey} dedup tuples. Plain\n * spaces and dashes can legally appear inside `file` names so the key\n * must use a separator that filenames cannot contain. `' <#> '` is\n * unambiguous, ASCII-clean (no control bytes — graph.ts had the same\n * class of bug with NUL delimiters), and obvious in diagnostic output.\n */\nconst CITATION_KEY_SEPARATOR = \" <#> \";\n\n/**\n * Flat citation shape consumed by `ContextPrimary.citations[]` AND by\n * the JSON export's `ExportPage.citations[]`. Exported so both\n * surfaces share one normalized shape rather than drifting — consumers\n * can reuse the same flattening rule across `llmwiki context` and\n * `llmwiki export`.\n */\nexport interface FlatCitation {\n  file: string;\n  start?: number;\n  end?: number;\n}\n\n/**\n * Materialized source window consumed by\n * `ContextPrimary.sourceWindows[]`. Always carries explicit line\n * numbers — Slice 4 only ever materializes claim-level spans, so\n * `start`/`end` are mandatory.\n */\ninterface SourceWindow {\n  file: string;\n  start: number;\n  end: number;\n  text: string;\n}\n\n/**\n * Flatten a page's `ClaimCitation[]` into the JSON-shape citation list.\n * Multi-source markers (`^[a.md, b.md]`) produce one object per span.\n * Paragraph-only citations stay (with no `start`/`end`).\n */\nexport function flattenCitations(citations: ClaimCitation[]): FlatCitation[] {\n  const out: FlatCitation[] = [];\n  const seen = new Set<string>();\n  for (const citation of citations) {\n    for (const span of citation.spans) {\n      const flat = toFlatCitation(span);\n      const key = citationKey(flat);\n      if (seen.has(key)) continue;\n      seen.add(key);\n      out.push(flat);\n    }\n  }\n  return out;\n}\n\n/** Lift one `SourceSpan` into the public flat shape. */\nfunction toFlatCitation(span: SourceSpan): FlatCitation {\n  if (!span.lines) return { file: span.file };\n  return { file: span.file, start: span.lines.start, end: span.lines.end };\n}\n\n/** Deduplication key. Uses `-` for missing line ranges; safe because lines are positive integers. */\nfunction citationKey(citation: FlatCitation): string {\n  const start = citation.start ?? \"-\";\n  const end = citation.end ?? \"-\";\n  return [citation.file, String(start), String(end)].join(CITATION_KEY_SEPARATOR);\n}\n\n/**\n * Per-pack source-window budget accumulator passed into\n * {@link materializeSourceWindows}. The orchestrator owns one\n * instance and shares it across all primary pages so the global\n * 20-window ceiling is enforced even when many pages each carry many\n * citations.\n */\ninterface SourceWindowBudget {\n  remaining: number;\n}\n\n/** Create a fresh budget seeded with the documented per-pack cap. */\nexport function createSourceWindowBudget(): SourceWindowBudget {\n  return { remaining: MAX_SOURCE_WINDOWS };\n}\n\n/**\n * Materialize source windows for one page's citations. Returns an\n * empty array when the citation list is empty, when no entries carry\n * line ranges (paragraph-only), or when the budget is exhausted.\n */\nexport async function materializeSourceWindows(\n  root: string,\n  citations: FlatCitation[],\n  budget: SourceWindowBudget,\n): Promise<SourceWindow[]> {\n  if (budget.remaining <= 0) return [];\n  const windows: SourceWindow[] = [];\n  for (const citation of citations) {\n    if (budget.remaining <= 0) break;\n    if (citation.start === undefined || citation.end === undefined) continue;\n    const window = await readSourceWindow(root, citation);\n    if (!window) continue;\n    windows.push(window);\n    budget.remaining -= 1;\n  }\n  return windows;\n}\n\n/** Read one source window or return null when the read is rejected by the path guard. */\nasync function readSourceWindow(\n  root: string,\n  citation: FlatCitation,\n): Promise<SourceWindow | null> {\n  if (citation.start === undefined || citation.end === undefined) return null;\n  const sourcesRoot = await resolveSourcesRoot(root);\n  if (!sourcesRoot) return null;\n  const realPath = await resolveSafePath(sourcesRoot, citation.file);\n  if (!realPath) return null;\n  return readClampedWindow(realPath, citation);\n}\n\n/**\n * Resolve the canonical `sources/` directory. Returns null when the\n * directory doesn't exist; otherwise returns the realpath so\n * `isInside` checks against canonical paths on platforms with\n * symlinked parents (macOS `/var` → `/private/var`, Linux container\n * bind mounts, etc.). Path confinement still rejects files whose\n * realpath escapes this canonical root, so a symlinked sources/ tree\n * remains safe.\n */\nasync function resolveSourcesRoot(root: string): Promise<string | null> {\n  const candidate = path.join(root, SOURCES_DIR);\n  try {\n    return await fs.realpath(candidate);\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Resolve `file` under `sourcesRoot`, rejecting:\n *   - absolute paths (`/etc/passwd`)\n *   - ANY `..` segment, even one that would normalize back inside\n *     sources/ (`nested/../paper.md` is rejected — the spec says\n *     \"reject parent traversal\", and \"looks safe after normalization\"\n *     is still traversal a reviewer must be able to spot in the raw\n *     citation marker)\n *   - paths whose realpath escapes `sourcesRoot` (symlinks pointing\n *     outside `sources/`)\n */\nasync function resolveSafePath(sourcesRoot: string, file: string): Promise<string | null> {\n  if (file.length === 0) return null;\n  if (path.isAbsolute(file)) return null;\n  if (containsParentSegment(file)) return null;\n  const joined = path.join(sourcesRoot, file);\n  const resolved = path.resolve(joined);\n  // Defense in depth: even after the segment guard, if the resolved\n  // path escapes sources/ (e.g., a Windows drive-letter trick or a\n  // separator we did not recognize) refuse it.\n  if (!isInside(sourcesRoot, resolved)) return null;\n  try {\n    const realPath = await fs.realpath(resolved);\n    if (!isInside(sourcesRoot, realPath)) return null;\n    return realPath;\n  } catch {\n    return null;\n  }\n}\n\n/**\n * True when any segment of `file` is literally `..`. Splits on BOTH\n * `/` and the platform separator so a malicious `nested\\..\\paper.md`\n * on Linux (where `\\` is a legal filename char) is still rejected when\n * served to a Windows agent reading the same context pack.\n */\nfunction containsParentSegment(file: string): boolean {\n  const segments = file.split(/[/\\\\]/);\n  return segments.some((segment) => segment === \"..\");\n}\n\n/**\n * True when `candidate` is `parent` itself or a descendant of it.\n * Adds a path separator suffix to `parent` before the prefix check so\n * `/parent` does not incorrectly contain `/parentish`.\n */\nfunction isInside(parent: string, candidate: string): boolean {\n  if (candidate === parent) return true;\n  const normalizedParent = parent.endsWith(path.sep) ? parent : `${parent}${path.sep}`;\n  return candidate.startsWith(normalizedParent);\n}\n\n/**\n * Read the requested line window, clamping to a maximum length so a\n * runaway citation cannot pull hundreds of lines into the pack. Both\n * `start` and `end` are 1-indexed inclusive (matching the\n * `SourceSpan` convention).\n */\nasync function readClampedWindow(\n  realPath: string,\n  citation: FlatCitation,\n): Promise<SourceWindow | null> {\n  if (citation.start === undefined || citation.end === undefined) return null;\n  let raw: string;\n  try {\n    raw = await fs.readFile(realPath, \"utf-8\");\n  } catch {\n    return null;\n  }\n  const lines = raw.split(/\\r?\\n/);\n  const startIndex = Math.max(0, citation.start - 1);\n  const inclusiveEnd = Math.min(lines.length, citation.end);\n  if (startIndex >= inclusiveEnd) return null;\n  const clampedEnd = Math.min(inclusiveEnd, startIndex + MAX_LINES_PER_WINDOW);\n  const text = lines.slice(startIndex, clampedEnd).join(\"\\n\");\n  return { file: citation.file, start: citation.start, end: startIndex + (clampedEnd - startIndex), text };\n}\n","/**\n * Multi-signal ranking for `llmwiki context`.\n *\n * Slice 1 wired lexical + exact-match signals. Slice 2 layers semantic\n * chunk retrieval on top of the same combiner (plan §Ranking Model);\n * the wrapper in `src/context/retrieval.ts` keeps the orchestrator\n * unaware of whether the embedding store contributed.\n *\n * Signals fed into the combiner:\n *   - `searchPages().results[].matchedIn` distinguishes title vs body\n *     hits without re-parsing the body.\n *   - Exact slug equality (case-insensitive after lowercasing) adds a\n *     strong bonus and the `exact-slug` reason.\n *   - Exact title equality (case-insensitive, trimmed) adds the\n *     strongest bonus and the `exact-title` reason.\n *   - Semantic chunk hits add a high-weight `semantic-chunk` reason\n *     and attach the chunk text/score/contentHash to the primary page;\n *     additional chunks on the same page contribute a capped bonus so\n *     a popular page can't shadow exact-title hits.\n *\n * Scores are normalized into [0, 1] best-effort — they're explainable\n * to the agent but not a quality guarantee. Stable tie-sort: descending\n * score, then ascending title, then ascending page ID.\n */\n\nimport { searchPages } from \"../viewer/search.js\";\nimport type { ViewerPage, ViewerSnapshot } from \"../viewer/types.js\";\nimport type { SemanticChunkHit } from \"./retrieval.js\";\nimport { flattenCitations } from \"./provenance.js\";\nimport type { ContextPrimary, PrimaryReason } from \"./types.js\";\n\n/** Per-signal weight (sums normalize so an exact-title hit lands near 1.0). */\nconst WEIGHT_TITLE_MATCH = 0.5;\nconst WEIGHT_BODY_MATCH = 0.3;\nconst WEIGHT_EXACT_SLUG = 0.4;\nconst WEIGHT_EXACT_TITLE = 0.5;\n\n/** Base weight for the first semantic chunk a page contributes. Peer of title-match. */\nconst WEIGHT_SEMANTIC_CHUNK = 0.5;\n/** Per-additional-chunk bonus once the first semantic hit on a page has landed. */\nconst WEIGHT_SEMANTIC_CHUNK_BONUS = 0.05;\n/** Max additional chunks (beyond the first) that contribute the per-chunk bonus. */\nconst MAX_SEMANTIC_BONUS_CHUNKS = 3;\n\n/** Cap so combined scores stay inside the normalized [0, 1] range. */\nconst MAX_NORMALIZED_SCORE = 1;\n\n/**\n * One semantic chunk surfaced for a primary page. Matches the inline\n * `ContextPrimary.chunks[]` shape in `types.ts`; declared locally so the\n * ranker can build it without exporting the structural anonymous type.\n */\ninterface PrimaryChunk {\n  text: string;\n  score: number;\n  contentHash: string;\n}\n\n/** Internal accumulator: one row per candidate page. */\ninterface RankingRow {\n  page: ViewerPage;\n  reasons: Set<PrimaryReason>;\n  weight: number;\n  snippet: string;\n  /** Chunks attached by `applySemanticSignals`; empty in lexical-only flows. */\n  chunks: PrimaryChunk[];\n}\n\n/**\n * Rank candidate pages for `prompt` against `snapshot`, returning up to\n * `topN` populated {@link ContextPrimary} entries.\n *\n * `semanticHits` is the post-retrieval chunk list from Slice 2; pass an\n * empty array (the default) for lexical-only behaviour. Citations and\n * sourceWindows stay empty in Slice 2 — those fields land in Slice 4.\n * Page-local `warnings` is sourced from the viewer collector.\n */\nexport function rankPages(\n  snapshot: ViewerSnapshot,\n  prompt: string,\n  topN: number,\n  semanticHits: SemanticChunkHit[] = [],\n): ContextPrimary[] {\n  const rows = new Map<string, RankingRow>();\n  applyLexicalSignals(rows, snapshot, prompt);\n  applyExactSignals(rows, snapshot, prompt);\n  applySemanticSignals(rows, snapshot, semanticHits);\n  const sorted = Array.from(rows.values()).sort(compareRows);\n  return sorted.slice(0, Math.max(0, topN)).map(rowToPrimary);\n}\n\n/** Push every `searchPages()` hit into the ranking map. */\nfunction applyLexicalSignals(\n  rows: Map<string, RankingRow>,\n  snapshot: ViewerSnapshot,\n  prompt: string,\n): void {\n  const { results } = searchPages(snapshot, prompt);\n  for (const result of results) {\n    const page = snapshot.pages.find((p) => p.id === result.id);\n    if (!page) continue;\n    const row = ensureRow(rows, page);\n    row.snippet = row.snippet || result.snippet;\n    if (result.matchedIn === \"title\") {\n      addReason(row, \"title-match\", WEIGHT_TITLE_MATCH);\n    } else {\n      addReason(row, \"body-match\", WEIGHT_BODY_MATCH);\n    }\n  }\n}\n\n/** Bonus pass for exact-slug and exact-title matches across all pages. */\nfunction applyExactSignals(\n  rows: Map<string, RankingRow>,\n  snapshot: ViewerSnapshot,\n  prompt: string,\n): void {\n  const normalized = prompt.trim().toLowerCase();\n  if (normalized.length === 0) return;\n  for (const page of snapshot.pages) {\n    if (page.slug.toLowerCase() === normalized) {\n      addReason(ensureRow(rows, page), \"exact-slug\", WEIGHT_EXACT_SLUG);\n    }\n    if (page.title.trim().toLowerCase() === normalized) {\n      addReason(ensureRow(rows, page), \"exact-title\", WEIGHT_EXACT_TITLE);\n    }\n  }\n}\n\n/**\n * Apply semantic chunk signals: each retrieved chunk is grouped by page\n * slug, the page gets the `semantic-chunk` reason once, a capped\n * multi-chunk bonus accrues for additional chunks on the same page, and\n * the chunk records are attached to the row for `primary[].chunks[]`.\n *\n * Chunks for slugs that no longer exist in the viewer snapshot are\n * dropped silently — the embedding store can lag behind page deletions\n * and we don't want to fabricate a phantom primary entry just because\n * the store carries a stale chunk.\n */\nfunction applySemanticSignals(\n  rows: Map<string, RankingRow>,\n  snapshot: ViewerSnapshot,\n  hits: SemanticChunkHit[],\n): void {\n  if (hits.length === 0) return;\n  const bySlug = groupHitsBySlug(hits);\n  for (const [slug, slugHits] of bySlug) {\n    const page = findPageBySlug(snapshot, slug);\n    if (!page) continue;\n    const row = ensureRow(rows, page);\n    addReason(row, \"semantic-chunk\", WEIGHT_SEMANTIC_CHUNK);\n    row.weight += semanticMultiChunkBonus(slugHits.length);\n    for (const hit of slugHits) {\n      row.chunks.push({\n        text: hit.text,\n        score: hit.score,\n        contentHash: hit.contentHash,\n      });\n    }\n  }\n}\n\n/** Group chunk hits by page slug while preserving the score-desc input order. */\nfunction groupHitsBySlug(hits: SemanticChunkHit[]): Map<string, SemanticChunkHit[]> {\n  const bySlug = new Map<string, SemanticChunkHit[]>();\n  for (const hit of hits) {\n    const existing = bySlug.get(hit.slug);\n    if (existing) existing.push(hit);\n    else bySlug.set(hit.slug, [hit]);\n  }\n  return bySlug;\n}\n\n/** Score bump for the 2nd..N-th chunk on the same page, capped. */\nfunction semanticMultiChunkBonus(chunkCount: number): number {\n  const extra = Math.max(0, Math.min(chunkCount - 1, MAX_SEMANTIC_BONUS_CHUNKS));\n  return extra * WEIGHT_SEMANTIC_CHUNK_BONUS;\n}\n\n/**\n * Resolve a bare chunk slug to a snapshot page, with concepts winning\n * over queries when both contain the same slug — matches the bare-slug\n * precedence rule used by the viewer's wikilink resolver.\n */\nfunction findPageBySlug(snapshot: ViewerSnapshot, slug: string): ViewerPage | null {\n  const concept = snapshot.pages.find(\n    (p) => p.pageDirectory === \"concepts\" && p.slug === slug,\n  );\n  if (concept) return concept;\n  const query = snapshot.pages.find(\n    (p) => p.pageDirectory === \"queries\" && p.slug === slug,\n  );\n  return query ?? null;\n}\n\n/** Fetch the row for `page`, lazily allocating it on first use. */\nfunction ensureRow(rows: Map<string, RankingRow>, page: ViewerPage): RankingRow {\n  const existing = rows.get(page.id);\n  if (existing) return existing;\n  const created: RankingRow = {\n    page,\n    reasons: new Set(),\n    weight: 0,\n    snippet: \"\",\n    chunks: [],\n  };\n  rows.set(page.id, created);\n  return created;\n}\n\n/** Record one reason + weight; reasons set de-dupes naturally. */\nfunction addReason(row: RankingRow, reason: PrimaryReason, weight: number): void {\n  row.reasons.add(reason);\n  row.weight += weight;\n}\n\n/** Stable sort: descending score, ascending title, ascending page ID. */\nfunction compareRows(a: RankingRow, b: RankingRow): number {\n  if (a.weight !== b.weight) return b.weight - a.weight;\n  const byTitle = a.page.title.localeCompare(b.page.title);\n  if (byTitle !== 0) return byTitle;\n  return a.page.id.localeCompare(b.page.id);\n}\n\n/**\n * Build the `warnings` array for a primary page, forwarding viewer-level\n * warnings and appending freshness-derived warnings for stale, contradicted,\n * and archived pages. These codes are context-only — the viewer surfaces\n * freshness as badges, not warnings. A page can carry multiple warnings\n * (e.g. stale AND contradicted → both codes appear).\n */\nfunction buildPrimaryWarnings(page: ViewerPage): ContextPrimary[\"warnings\"] {\n  const warnings = page.warnings.map((w) => ({ code: w.code, message: w.message }));\n  if (page.freshness.freshnessStatus === \"stale\") {\n    warnings.push({\n      code: \"stale-page\",\n      message:\n        \"A source this page was compiled from has changed since the last compile; treat with caution.\",\n    });\n  }\n  if (page.freshness.contradicted) {\n    warnings.push({\n      code: \"contradicted-page\",\n      message: \"This page is contradicted by another page; treat its claims with caution.\",\n    });\n  }\n  if (page.freshness.archived) {\n    warnings.push({\n      code: \"archived-page\",\n      message: \"This page is archived and may be outdated or deprecated.\",\n    });\n  }\n  return warnings;\n}\n\n/**\n * Convert a ranking row into a ContextPrimary.\n *\n * Slice 4 fills `citations` from the viewer collector's already-parsed\n * `ClaimCitation[]` (one object per source span, paragraph-only spans\n * keep no line range, multi-source markers split, deduped by\n * `(file,start,end)`, document-order preserved).\n *\n * Page-local `warnings` was wired in Slice 1; it forwards the same\n * `ViewerWarning` objects the viewer surfaces, so any malformed-frontmatter\n * or unresolved-citation diagnostic the viewer already knows about\n * lands in the context pack automatically. A `stale-page` warning is\n * synthesized here when the page's freshness status is `stale`.\n *\n * `sourceWindows` stays empty here — the orchestrator owns the\n * per-pack budget and writes windows back into the primary entries\n * after ranking, so the ranker remains a pure function over the\n * snapshot.\n */\nfunction rowToPrimary(row: RankingRow): ContextPrimary {\n  const { freshness } = row.page;\n  return {\n    id: row.page.id,\n    title: row.page.title,\n    pageDirectory: row.page.pageDirectory,\n    score: normalizeWeight(row.weight),\n    reasons: Array.from(row.reasons).sort(),\n    summary: row.snippet,\n    chunks: row.chunks,\n    citations: flattenCitations(row.page.citations),\n    sourceWindows: [],\n    warnings: buildPrimaryWarnings(row.page),\n    freshnessStatus: freshness.freshnessStatus,\n    contradicted: freshness.contradicted,\n    archived: freshness.archived,\n  };\n}\n\n/** Squash accumulated weight into [0, 1] without inventing precision. */\nfunction normalizeWeight(weight: number): number {\n  if (weight <= 0) return 0;\n  if (weight >= MAX_NORMALIZED_SCORE) return MAX_NORMALIZED_SCORE;\n  return Math.round(weight * 100) / 100;\n}\n","/**\n * Semantic retrieval wrapper for `llmwiki context` Slice 2.\n *\n * Wraps `readEmbeddingStore()` + `findRelevantChunks()` so the\n * orchestrator never has to special-case provider failures, missing\n * stores, or stale-model stores. Semantic retrieval is opportunistic\n * here — context packs must keep working on lexical signals alone when\n * the embedding store is absent OR the active provider has no\n * credentials. The wrapper translates both failure modes into stable\n * warning codes (`embedding-store-missing` / `query-embedding-unavailable`)\n * so the JSON contract stays predictable for agents regardless of which\n * branch fired.\n *\n * Stale-model stores are folded into the `embedding-store-missing`\n * branch. We detect them HERE — not by waiting for `findRelevantChunks`\n * to return `[]` — because the embeddings module emits a\n * `output.status(\"!\", ...)` warning to stdout via `console.log` when\n * `loadActiveStore` sees a stale model. That leak would corrupt\n * `llmwiki context --json` output (stdout must be pure JSON). Catching\n * the model mismatch up front avoids the embeddings module's warning\n * path entirely.\n *\n * Malformed embedding store files (truncated writes, hand-edits, etc.)\n * are also folded into `embedding-store-missing` rather than propagated\n * as crashes. `readEmbeddingStore` does not catch its own JSON parse\n * failures, so the wrapper guards both the read and the parse so\n * `context` keeps producing parseable output even when the store on\n * disk is broken.\n */\n\nimport {\n  findRelevantChunks,\n  readEmbeddingStore,\n  resolveEmbeddingModel,\n} from \"../utils/embeddings.js\";\nimport type { EmbeddingStore } from \"../utils/embeddings.js\";\n\n/** Stable warning code returned when semantic retrieval did not contribute. */\nexport type SemanticRetrievalWarning =\n  | \"embedding-store-missing\"\n  | \"query-embedding-unavailable\"\n  | \"semantic-retrieval-error\";\n\n/**\n * Slimmed chunk record passed from retrieval into ranking. Keeps\n * `ranking.ts` independent of the underlying `ChunkEmbeddingEntry`\n * shape so the embedding store can evolve without churn here.\n */\nexport interface SemanticChunkHit {\n  /** Source page slug; bare-slug resolved against the viewer snapshot in ranking. */\n  slug: string;\n  /** Chunk body text — surfaced verbatim in `primary[].chunks[].text`. */\n  text: string;\n  /** Cosine similarity from `findTopKChunks`; pass-through into the chunk entry. */\n  score: number;\n  /** Stable hash of the chunk text; pass-through into the chunk entry. */\n  contentHash: string;\n}\n\n/**\n * Outcome of one semantic retrieval call. Either `hits` is populated and\n * `warning` is `null`, or `hits` is empty and `warning` carries the\n * stable code. We use mutually-exclusive null/value rather than a tagged\n * union so callers can spread both fields into the envelope without\n * widening narrow types.\n */\nexport interface SemanticRetrievalOutcome {\n  hits: SemanticChunkHit[];\n  warning: SemanticRetrievalWarning | null;\n}\n\n/**\n * Best-effort semantic retrieval. Returns the top-k chunks the active\n * embedding store can offer for `prompt`, OR a warning that explains\n * why semantic retrieval contributed nothing this call.\n *\n * Precondition: caller already knows the original prompt should be\n * passed (not the truncated display copy). Slice 2 wires the orchestrator\n * to pass `NormalizedOptions.rankingPrompt`.\n */\nexport async function retrieveSemanticChunks(\n  root: string,\n  prompt: string,\n  topChunks: number,\n): Promise<SemanticRetrievalOutcome> {\n  if (topChunks <= 0) return emptyOutcome(null);\n  if (await isStoreUnusable(root)) return emptyOutcome(\"embedding-store-missing\");\n\n  let raw: Awaited<ReturnType<typeof findRelevantChunks>>;\n  try {\n    raw = await findRelevantChunks(root, prompt, topChunks);\n  } catch (err) {\n    // Provider/config failures are expected in credential-free context\n    // runs. Unknown exceptions still fall back to lexical, but receive\n    // a distinct warning so real bugs are not mislabeled as auth.\n    return emptyOutcome(classifyRetrievalError(err));\n  }\n\n  if (raw.length === 0) {\n    // Defensive: with the upfront stale-model + chunk-count checks the\n    // only way to land here is a TOCTOU race where the store changed\n    // between the pre-check read and `findRelevantChunks`. Surface as\n    // `embedding-store-missing` so the warning vocabulary stays small.\n    return emptyOutcome(\"embedding-store-missing\");\n  }\n\n  return { hits: raw.map(toSemanticChunkHit), warning: null };\n}\n\n/** Build the empty-hits outcome shape; centralised to keep callers terse. */\nfunction emptyOutcome(warning: SemanticRetrievalWarning | null): SemanticRetrievalOutcome {\n  return { hits: [], warning };\n}\n\n/**\n * True when the on-disk embedding store cannot supply chunks: file\n * missing, JSON malformed, v1 / empty v2 store, OR built with a\n * different embedding model than the active provider is using.\n *\n * The stale-model check MUST happen here (before any `findRelevantChunks`\n * call) so the embeddings module's stale-store warning — which writes\n * to stdout via `output.status` — never fires. That warning would\n * corrupt `--json` output. Same reasoning applies to malformed-JSON\n * reads: `readEmbeddingStore` lets `JSON.parse` throw, which would\n * crash the command with exit 1 unless we catch it here.\n */\nasync function isStoreUnusable(root: string): Promise<boolean> {\n  const store = await tryReadEmbeddingStore(root);\n  if (!store) return true;\n  if (!store.chunks || store.chunks.length === 0) return true;\n  if (isStaleModel(store)) return true;\n  return false;\n}\n\n/**\n * Wrap `readEmbeddingStore` so a missing OR malformed file both reduce\n * to `null`. The reader does `await readFile` + `JSON.parse` without\n * its own catch, so a broken store would otherwise surface as an\n * unhandled rejection to the caller.\n */\nasync function tryReadEmbeddingStore(root: string): Promise<EmbeddingStore | null> {\n  try {\n    return await readEmbeddingStore(root);\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Compare the persisted store's embedding model against the active\n * provider's resolved model. Returns true when they disagree so the\n * caller can fall back without triggering the embeddings module's\n * stdout warning. Defensive: a thrown `resolveEmbeddingModel` (e.g.\n * unknown `LLMWIKI_PROVIDER`) is also treated as stale.\n */\nfunction isStaleModel(store: EmbeddingStore): boolean {\n  try {\n    return store.model !== resolveEmbeddingModel();\n  } catch {\n    return true;\n  }\n}\n\n/** Classify failures without leaking raw provider or stack text into JSON. */\nfunction classifyRetrievalError(err: unknown): SemanticRetrievalWarning {\n  const message = err instanceof Error ? err.message : String(err);\n  return looksLikeProviderFailure(message)\n    ? \"query-embedding-unavailable\"\n    : \"semantic-retrieval-error\";\n}\n\n/** Known provider/config/network failures that should keep the legacy warning code. */\nfunction looksLikeProviderFailure(message: string): boolean {\n  return /api[_ -]?key|auth|credential|token|provider|voyage|openai|ollama|timeout|fetch|econn|enotfound/i\n    .test(message);\n}\n\n/** Project an embedding-store chunk hit onto the ranking-facing shape. */\nfunction toSemanticChunkHit(\n  raw: Awaited<ReturnType<typeof findRelevantChunks>>[number],\n): SemanticChunkHit {\n  return {\n    slug: raw.chunk.slug,\n    text: raw.chunk.text,\n    score: raw.score,\n    contentHash: raw.chunk.contentHash,\n  };\n}\n","/**\n * Graph neighborhood expansion for `llmwiki context` Slice 3.\n *\n * Pure function over `ViewerSnapshot.graph` (built once at snapshot\n * time by `src/viewer/graph.ts::buildGraphData`) plus the orchestrator's\n * resolved primary IDs. Returns the documented `neighbors[]` and\n * `gaps[]` arrays without rebuilding adjacency from disk and without\n * touching the embeddings store.\n *\n * Topology rules pinned by the implementation plan §Graph Expansion:\n *   - real-page-only neighbors (ghosts go to `gaps[]` instead, with\n *     `code: \"dangling-link\"` and `pageId` set to the page that linked\n *     to the missing target)\n *   - primary pages never appear in `neighbors[]`\n *   - bidirectional edges (A->B and B->A) collapse to a single neighbor\n *     entry via the canonical unordered key `(min(a,b), max(a,b))`\n *   - depth 1 expands directly from each primary page\n *   - depth 2 expands from surviving depth-1 real neighbors, skipping\n *     primary back-edges and pages already at depth 1; cycles are\n *     blocked by a visited set\n *   - `--no-neighbors` and `--depth 0` produce empty `neighbors` /\n *     `gaps` arrays without crashing\n *\n * Scores are deterministic and normalized into [0, 1]; direct neighbors\n * outrank second-hop, pages with multiple primary connections get a\n * small additive bonus, and same-kind page pairs get a smaller schema\n * affinity bonus. Stable tie-sort: descending score, then\n * ascending `to` page id (Slice 3 does not have neighbor titles handy\n * without an extra lookup, and id is already monotonic per directory).\n */\n\nimport type {\n  GraphData,\n  GraphNode,\n  PageId,\n  ViewerPage,\n} from \"../viewer/types.js\";\n\n/** Closed v1 neighbor edge label. */\nconst NEIGHBOR_REASON_WIKILINK = \"wikilink\";\n\n/**\n * Delimiter joining the two PageIds in a canonical pair key. Visible\n * ASCII (not a control byte) so the source file stays free of NUL\n * bytes that confuse grep/fallow/git tooling, and the substring\n * \" <-> \" cannot collide with any directory/slug character allowed in\n * a `PageId` (`concepts/<slug>` / `queries/<slug>`).\n */\nconst CANONICAL_PAIR_SEPARATOR = \" <-> \";\n\n/**\n * Hard cap on the total number of emitted neighbor entries (depth-1 +\n * depth-2 combined). Applied BEFORE depth-2 expansion so a high-degree\n * primary page cannot blow the context pack open by way of fan-out\n * through trimmed depth-1 bridges. Re-applied at the end so the\n * sorted, merged output never exceeds the bound either.\n */\nconst MAX_GRAPH_NEIGHBORS = 20;\n\n/** Base score for a direct (depth-1) neighbor edge. */\nconst WEIGHT_NEIGHBOR_DIRECT = 0.5;\n\n/** Base score for a second-hop (depth-2) neighbor edge. */\nconst WEIGHT_NEIGHBOR_SECOND_HOP = 0.25;\n\n/**\n * Additive bonus per additional primary connection beyond the first\n * (capped). Keeps centrally-linked neighbors above peripherally-linked\n * ones without letting a \"popular\" page accumulate unbounded weight.\n */\nconst WEIGHT_PRIMARY_CONNECTION_BONUS = 0.05;\nconst MAX_PRIMARY_CONNECTION_BONUS_HITS = 3;\n\n/** Small schema-affinity bump when both endpoints share the same page kind. */\nconst WEIGHT_SAME_KIND_BONUS = 0.03;\nconst DEFAULT_PAGE_KIND = \"concept\";\n\n/** Cap so combined scores stay inside the normalized [0, 1] range. */\nconst MAX_NORMALIZED_SCORE = 1;\n\n/** Reasons set on emitted neighbor entries. Closed v1 enum. */\ntype NeighborReason = typeof NEIGHBOR_REASON_WIKILINK;\n\n/** Direction of the underlying wikilink relative to `from`. */\ntype NeighborDirection = \"outgoing\" | \"incoming\";\n\n/** One neighbor entry in the v1 context-pack envelope. */\ninterface GraphNeighbor {\n  from: PageId;\n  to: PageId;\n  direction: NeighborDirection;\n  distance: number;\n  score: number;\n  reason: NeighborReason;\n}\n\n/** Gap entry surfaced when a primary page links to a missing target. */\ninterface GraphGap {\n  code: \"dangling-link\";\n  message: string;\n  pageId: PageId;\n}\n\n/** Output of {@link expandGraphNeighborhood}. */\nexport interface GraphExpansionOutput {\n  neighbors: GraphNeighbor[];\n  gaps: GraphGap[];\n}\n\n/** Inputs grouped to keep argument lists short. */\ninterface GraphExpansionInput {\n  graph: GraphData;\n  pages: ViewerPage[];\n  primaryIds: ReadonlySet<PageId>;\n  /** 0 = expansion off; 1 = direct only; 2 = direct + second-hop. */\n  depth: number;\n}\n\n/**\n * Expand `primaryIds` into the documented `{ neighbors, gaps }` shape.\n * Returns empty arrays — never `undefined`/`null` — so the orchestrator\n * can splice the result into the JSON envelope unconditionally.\n */\nexport function expandGraphNeighborhood(\n  input: GraphExpansionInput,\n): GraphExpansionOutput {\n  // Depth 0 OR no primary IDs: both `neighbors[]` and `gaps[]` stay\n  // empty (plan §CLI Acceptance Criteria). `--no-neighbors` short-\n  // circuits before this function is called; this branch covers\n  // `--depth 0` and the empty-wiki path.\n  if (input.depth <= 0 || input.primaryIds.size === 0) {\n    return { neighbors: [], gaps: [] };\n  }\n  const adjacency = buildAdjacency(input.graph);\n  const ghostIds = collectGhostIds(input.graph.nodes);\n  const pageKinds = buildPageKindMap(input.pages);\n  // Sort + cap depth-1 BEFORE depth-2 expansion so a trimmed-out\n  // bridge can never contribute second-hop emissions. Without this\n  // gate, a primary page with high fan-out could fan out further at\n  // depth 2 and balloon `neighbors[]` past the documented cap.\n  const depth1Raw = expandDepthOne({\n    primaryIds: input.primaryIds,\n    adjacency,\n    ghostIds,\n    pageKinds,\n  });\n  const depth1 = depth1Raw.sort(compareNeighbors).slice(0, MAX_GRAPH_NEIGHBORS);\n  const depth2 = input.depth >= 2\n    ? expandDepthTwo({\n        primaryIds: input.primaryIds,\n        adjacency,\n        ghostIds,\n        pageKinds,\n        depthOneTargets: collectDepthOneTargets(depth1),\n      })\n    : [];\n  // Re-cap after merging so depth-2 entries cannot push the total\n  // above the bound either. Direct (distance 1) entries outrank\n  // second-hop in the comparator so the trim drops second-hop first.\n  const neighbors = [...depth1, ...depth2]\n    .sort(compareNeighbors)\n    .slice(0, MAX_GRAPH_NEIGHBORS);\n  return { neighbors, gaps: emitGapsFromPrimary(input) };\n}\n\n/** Surface dangling-link gaps for every primary page that owns one. */\nfunction emitGapsFromPrimary(input: GraphExpansionInput): GraphGap[] {\n  const gaps: GraphGap[] = [];\n  for (const page of input.pages) {\n    if (!input.primaryIds.has(page.id)) continue;\n    for (const dangling of page.danglingLinks ?? []) {\n      gaps.push({\n        code: \"dangling-link\",\n        message: `Page links to [[${dangling.display}]], but no page exists.`,\n        pageId: page.id,\n      });\n    }\n  }\n  return gaps;\n}\n\n/** Outgoing + incoming edge maps for fast neighbor lookup keyed by PageId. */\ninterface Adjacency {\n  outgoing: Map<PageId, Set<PageId>>;\n  incoming: Map<PageId, Set<PageId>>;\n}\n\n/** Build the bidirectional adjacency from the snapshot's edge list. */\nfunction buildAdjacency(graph: GraphData): Adjacency {\n  const outgoing = new Map<PageId, Set<PageId>>();\n  const incoming = new Map<PageId, Set<PageId>>();\n  for (const edge of graph.edges) {\n    addToSetMap(outgoing, edge.source, edge.target);\n    addToSetMap(incoming, edge.target, edge.source);\n  }\n  return { outgoing, incoming };\n}\n\n/** Insert `value` into the set at `key`, creating the set on first use. */\nfunction addToSetMap<K, V>(map: Map<K, Set<V>>, key: K, value: V): void {\n  const existing = map.get(key);\n  if (existing) existing.add(value);\n  else map.set(key, new Set([value]));\n}\n\n/** Collect every ghost-node id so we can drop dangling targets from neighbors. */\nfunction collectGhostIds(nodes: GraphNode[]): Set<PageId> {\n  const ghosts = new Set<PageId>();\n  for (const node of nodes) if (node.isDangling) ghosts.add(node.id);\n  return ghosts;\n}\n\n/** Shared input for the depth-1 expansion path. */\ninterface DepthOneInput {\n  primaryIds: ReadonlySet<PageId>;\n  adjacency: Adjacency;\n  ghostIds: ReadonlySet<PageId>;\n  pageKinds: ReadonlyMap<PageId, string>;\n}\n\n/**\n * Depth-1 expansion: for each primary page, walk outgoing + incoming\n * edges and emit one entry per real-page neighbor. Bidirectional\n * duplicates collapse via the canonical-pair key.\n */\nfunction expandDepthOne(input: DepthOneInput): GraphNeighbor[] {\n  const emitted = new Map<string, GraphNeighbor>();\n  const connectionCount = new Map<PageId, number>();\n  for (const primary of input.primaryIds) {\n    addNeighborsForPrimary({ ...input, primary, emitted, connectionCount });\n  }\n  applyPrimaryConnectionBonus(emitted, connectionCount);\n  return Array.from(emitted.values());\n}\n\n/** Helpers passed into the per-primary depth-1 walker. */\ninterface DepthOnePerPrimary extends DepthOneInput {\n  primary: PageId;\n  emitted: Map<string, GraphNeighbor>;\n  connectionCount: Map<PageId, number>;\n}\n\n/** Walk every edge incident to one primary page and emit canonicalized neighbors. */\nfunction addNeighborsForPrimary(ctx: DepthOnePerPrimary): void {\n  walkIncidentEdges(ctx.adjacency, ctx.primary, (other, direction) => {\n    tryEmitDirect({ ctx, other, direction });\n  });\n}\n\n/** Inputs for the per-edge depth-1 emission check. */\ninterface EmitDirectInput {\n  ctx: DepthOnePerPrimary;\n  other: PageId;\n  direction: NeighborDirection;\n}\n\n/**\n * Emit a depth-1 neighbor edge if it survives the no-ghost / no-primary\n * / canonical-key filters. Bumps the per-target connection counter\n * either way so multi-primary connections get the documented bonus\n * even when the second edge would otherwise be skipped as a duplicate.\n */\nfunction tryEmitDirect(input: EmitDirectInput): void {\n  const { ctx, other, direction } = input;\n  if (ctx.ghostIds.has(other)) return;\n  if (ctx.primaryIds.has(other)) return;\n  bumpConnection(ctx.connectionCount, other);\n  mergeOrInsertNeighbor(ctx.emitted, {\n    from: ctx.primary,\n    to: other,\n    direction,\n    distance: 1,\n    score: scoreWithSameKindBonus(\n      WEIGHT_NEIGHBOR_DIRECT,\n      ctx.primary,\n      other,\n      ctx.pageKinds,\n    ),\n  });\n}\n\n/** Increment the per-target connection counter (used for the multi-primary bonus). */\nfunction bumpConnection(counter: Map<PageId, number>, target: PageId): void {\n  counter.set(target, (counter.get(target) ?? 0) + 1);\n}\n\n/** Empty PageId set reused across walks to avoid allocating per call. */\nconst EMPTY_NEIGHBOR_SET: ReadonlySet<PageId> = new Set<PageId>();\n\n/**\n * Walk every wikilink edge incident to `node` and invoke `onEdge` with\n * the other endpoint plus the direction relative to `node`. Centralised\n * so depth-1 and depth-2 walkers share the outgoing-then-incoming\n * iteration order without copy-pasting the boilerplate.\n */\nfunction walkIncidentEdges(\n  adjacency: Adjacency,\n  node: PageId,\n  onEdge: (other: PageId, direction: NeighborDirection) => void,\n): void {\n  const outgoing = adjacency.outgoing.get(node) ?? EMPTY_NEIGHBOR_SET;\n  const incoming = adjacency.incoming.get(node) ?? EMPTY_NEIGHBOR_SET;\n  for (const target of outgoing) onEdge(target, \"outgoing\");\n  for (const source of incoming) onEdge(source, \"incoming\");\n}\n\n/** Candidate neighbor about to be merged into the canonical-key map. */\ninterface NeighborCandidate {\n  from: PageId;\n  to: PageId;\n  direction: NeighborDirection;\n  distance: number;\n  score: number;\n}\n\n/**\n * Insert `candidate` into `emitted` under its canonical-pair key OR,\n * if an entry for that pair already exists, promote its direction\n * from `incoming` to `outgoing` when this edge represents the natural\n * `from -> to` link. The dedup keeps bidirectional pairs (A->B AND\n * B->A) collapsed to a single neighbor entry per the plan.\n */\nfunction mergeOrInsertNeighbor(\n  emitted: Map<string, GraphNeighbor>,\n  candidate: NeighborCandidate,\n): void {\n  const key = canonicalPairKey(candidate.from, candidate.to);\n  const existing = emitted.get(key);\n  if (existing) {\n    if (existing.direction === \"incoming\" && candidate.direction === \"outgoing\") {\n      existing.direction = \"outgoing\";\n    }\n    return;\n  }\n  emitted.set(key, { ...candidate, reason: NEIGHBOR_REASON_WIKILINK });\n}\n\n/**\n * After every primary contributes, apply the per-additional-connection\n * score bonus to each neighbor entry. The first connection is the base\n * weight; only the 2nd..(MAX+1)-th add the per-hit bonus.\n */\nfunction applyPrimaryConnectionBonus(\n  emitted: Map<string, GraphNeighbor>,\n  connectionCount: Map<PageId, number>,\n): void {\n  for (const neighbor of emitted.values()) {\n    const hits = connectionCount.get(neighbor.to) ?? 0;\n    const extraHits = Math.min(\n      Math.max(0, hits - 1),\n      MAX_PRIMARY_CONNECTION_BONUS_HITS,\n    );\n    neighbor.score = clampScore(\n      neighbor.score + extraHits * WEIGHT_PRIMARY_CONNECTION_BONUS,\n    );\n  }\n}\n\n/** Inputs for depth-2 expansion. */\ninterface DepthTwoInput {\n  primaryIds: ReadonlySet<PageId>;\n  adjacency: Adjacency;\n  ghostIds: ReadonlySet<PageId>;\n  pageKinds: ReadonlyMap<PageId, string>;\n  depthOneTargets: ReadonlySet<PageId>;\n}\n\n/**\n * Depth-2 expansion: walk from each surviving depth-1 neighbor and\n * emit edges to NEW real pages (not primary, not already at depth 1,\n * not ghosts). Bidirectional pairs at depth 2 also collapse via the\n * canonical-pair key. Back-edges to primary are dropped because that\n * relationship is already represented by the primary's depth-1 entry.\n */\nfunction expandDepthTwo(input: DepthTwoInput): GraphNeighbor[] {\n  const emitted = new Map<string, GraphNeighbor>();\n  for (const bridge of input.depthOneTargets) {\n    walkDepthTwoFromBridge({ ...input, bridge, emitted });\n  }\n  return Array.from(emitted.values());\n}\n\n/** Per-bridge depth-2 walker context; bridge is the depth-1 neighbor we expand from. */\ninterface DepthTwoPerBridge extends DepthTwoInput {\n  bridge: PageId;\n  emitted: Map<string, GraphNeighbor>;\n}\n\n/** Walk every edge incident to one depth-1 bridge node. */\nfunction walkDepthTwoFromBridge(ctx: DepthTwoPerBridge): void {\n  walkIncidentEdges(ctx.adjacency, ctx.bridge, (other, direction) => {\n    tryEmitSecondHop({ ctx, other, direction });\n  });\n}\n\n/** Inputs for the per-edge depth-2 emission check. */\ninterface EmitSecondHopInput {\n  ctx: DepthTwoPerBridge;\n  other: PageId;\n  direction: NeighborDirection;\n}\n\n/**\n * Emit a depth-2 neighbor edge if the target is a real page that is\n * neither primary nor already in the depth-1 neighbor set. Same\n * canonical-key de-dupe rule as depth 1; direction prefers outgoing\n * on bidirectional collisions to keep the natural reading order.\n */\nfunction tryEmitSecondHop(input: EmitSecondHopInput): void {\n  const { ctx, other, direction } = input;\n  if (ctx.ghostIds.has(other)) return;\n  if (ctx.primaryIds.has(other)) return;\n  if (ctx.depthOneTargets.has(other)) return;\n  mergeOrInsertNeighbor(ctx.emitted, {\n    from: ctx.bridge,\n    to: other,\n    direction,\n    distance: 2,\n    score: scoreWithSameKindBonus(\n      WEIGHT_NEIGHBOR_SECOND_HOP,\n      ctx.bridge,\n      other,\n      ctx.pageKinds,\n    ),\n  });\n}\n\n/** Map page ID to schema/page kind, defaulting legacy pages to concept. */\nfunction buildPageKindMap(pages: ViewerPage[]): Map<PageId, string> {\n  const kinds = new Map<PageId, string>();\n  for (const page of pages) {\n    const kind = page.frontmatter.kind;\n    kinds.set(page.id, typeof kind === \"string\" && kind.length > 0 ? kind : DEFAULT_PAGE_KIND);\n  }\n  return kinds;\n}\n\n/** Add the small kind-affinity bonus when both real endpoints share a kind. */\nfunction scoreWithSameKindBonus(\n  base: number,\n  from: PageId,\n  to: PageId,\n  pageKinds: ReadonlyMap<PageId, string>,\n): number {\n  return samePageKind(from, to, pageKinds)\n    ? clampScore(base + WEIGHT_SAME_KIND_BONUS)\n    : base;\n}\n\n/** True when both endpoints have an equal page kind in the real-page map. */\nfunction samePageKind(\n  from: PageId,\n  to: PageId,\n  pageKinds: ReadonlyMap<PageId, string>,\n): boolean {\n  const fromKind = pageKinds.get(from);\n  const toKind = pageKinds.get(to);\n  return fromKind !== undefined && toKind !== undefined && fromKind === toKind;\n}\n\n/** Collect just the `to` ids from a depth-1 neighbor list for fast lookups. */\nfunction collectDepthOneTargets(neighbors: GraphNeighbor[]): Set<PageId> {\n  const ids = new Set<PageId>();\n  for (const n of neighbors) ids.add(n.to);\n  return ids;\n}\n\n/**\n * Canonical key for an unordered page pair so A->B and B->A collapse\n * to a single neighbor entry. `String.localeCompare` keeps the\n * ordering platform-stable for any unicode-bearing PageId.\n */\nfunction canonicalPairKey(a: PageId, b: PageId): string {\n  return a < b\n    ? `${a}${CANONICAL_PAIR_SEPARATOR}${b}`\n    : `${b}${CANONICAL_PAIR_SEPARATOR}${a}`;\n}\n\n/** Squash a score into [0, 1] without inventing precision. */\nfunction clampScore(weight: number): number {\n  if (weight <= 0) return 0;\n  if (weight >= MAX_NORMALIZED_SCORE) return MAX_NORMALIZED_SCORE;\n  return Math.round(weight * 100) / 100;\n}\n\n/**\n * Stable sort: descending score, then ascending `to` id. We don't have\n * neighbor titles at this layer; the namespaced PageId already sorts\n * deterministically per directory so agents see a fixed ordering.\n */\nfunction compareNeighbors(a: GraphNeighbor, b: GraphNeighbor): number {\n  if (a.score !== b.score) return b.score - a.score;\n  return a.to.localeCompare(b.to);\n}\n","/**\n * Token budget estimation + deterministic trimming for `llmwiki context`.\n *\n * V1 uses a deterministic `Math.ceil(chars / 4)` heuristic so the token\n * count is stable across runs and identical between CLI and MCP. The\n * helper is isolated so a real tokenizer can replace it later without\n * touching the orchestrator (see plan §Budgeting).\n *\n * The estimator is intentionally pessimistic on the high side: a 4-char\n * average is slightly low for English prose, so packets that pass\n * `estimatedTokens <= requestedTokens` will fit comfortably in a real\n * tokenizer's count as well.\n *\n * Trimming order (plan §Budgeting §Trimming order):\n *   1. neighbors\n *   2. source windows\n *   3. semantic chunks / excerpts\n *   4. primary pages (last resort)\n *\n * Trim functions mutate a deep-cloned copy of the pack so the caller's\n * draft is never observably modified. JSON validity is preserved at\n * every step because we drop entire array elements rather than\n * surgically slicing strings.\n */\n\nimport type { ContextBudget, ContextPack } from \"./types.js\";\n\n/** Average chars-per-token used by the cheap heuristic. */\nconst APPROX_CHARS_PER_TOKEN = 4;\n\n/** Section names that can land in `budget.trimmedSections`. */\ntype TrimmedSection = \"neighbors\" | \"sourceWindows\" | \"chunks\" | \"primary\";\n\n/**\n * Estimate token count for an arbitrary string. Always returns a\n * non-negative integer. The empty string and `null`/`undefined` map to\n * zero; non-string inputs are coerced.\n */\nexport function estimateTokens(text: unknown): number {\n  if (text === null || text === undefined) return 0;\n  const stringified = typeof text === \"string\" ? text : String(text);\n  if (stringified.length === 0) return 0;\n  return Math.ceil(stringified.length / APPROX_CHARS_PER_TOKEN);\n}\n\n/**\n * Estimate the total token weight of a serialized context pack. Uses\n * the same heuristic as {@link estimateTokens}; runs on the\n * already-rendered JSON string so trimming decisions can iterate\n * without rebuilding the structured envelope from scratch.\n */\nexport function estimatePackTokens(pack: ContextPack): number {\n  return estimateTokens(JSON.stringify(pack));\n}\n\n/**\n * Build a fresh budget envelope before estimation/trimming runs.\n * Defaults preserve the v1 contract (`truncated: false`,\n * `trimmedSections: []`); the orchestrator overwrites these in\n * `finalizeBudget` once trimming decisions are known.\n */\nexport function buildBudget(requestedTokens: number, estimatedTokens: number): ContextBudget {\n  return {\n    requestedTokens,\n    estimatedTokens,\n    truncated: false,\n    trimmedSections: [],\n  };\n}\n\n/** Result returned by {@link trimToBudget}; pack is a NEW object, never the input. */\ninterface TrimResult {\n  pack: ContextPack;\n  trimmedSections: TrimmedSection[];\n}\n\n/**\n * Deterministically trim `pack` until `estimatePackTokens(pack) <=\n * requestedTokens`, in the documented order:\n *   neighbors -> sourceWindows -> chunks -> primary\n *\n * Each section is drained from the END of its array so the highest-\n * scored entries survive longest (ranking output is already sorted\n * descending). The returned pack is always a deep clone — the caller's\n * draft is left untouched.\n *\n * If the minimal envelope (no neighbors, no sourceWindows, no chunks,\n * no primary) still exceeds the budget, the pack is returned as-is\n * with `trimmedSections` listing every section we touched so consumers\n * can see the failure mode.\n */\nexport function trimToBudget(pack: ContextPack, requestedTokens: number): TrimResult {\n  const clone = clonePack(pack);\n  const trimmed = new Set<TrimmedSection>();\n  if (estimatePackTokens(clone) <= requestedTokens) {\n    return { pack: clone, trimmedSections: [] };\n  }\n  trimNeighbors(clone, requestedTokens, trimmed);\n  trimSourceWindows(clone, requestedTokens, trimmed);\n  trimChunks(clone, requestedTokens, trimmed);\n  trimPrimary(clone, requestedTokens, trimmed);\n  return { pack: clone, trimmedSections: orderedSections(trimmed) };\n}\n\n/** Deep-clone via `structuredClone` so per-step mutations cannot leak. */\nfunction clonePack(pack: ContextPack): ContextPack {\n  return structuredClone(pack);\n}\n\n/** Re-emit trimmed sections in the documented trim order, not insertion order. */\nfunction orderedSections(trimmed: Set<TrimmedSection>): TrimmedSection[] {\n  const order: TrimmedSection[] = [\"neighbors\", \"sourceWindows\", \"chunks\", \"primary\"];\n  return order.filter((section) => trimmed.has(section));\n}\n\n/** Drop neighbors from the end of the sorted list until the pack fits or none remain. */\nfunction trimNeighbors(\n  pack: ContextPack,\n  budget: number,\n  trimmed: Set<TrimmedSection>,\n): void {\n  while (pack.neighbors.length > 0 && estimatePackTokens(pack) > budget) {\n    pack.neighbors.pop();\n    trimmed.add(\"neighbors\");\n  }\n}\n\n/**\n * Drop source windows page-by-page from the bottom-ranked primary\n * entry first so the most relevant page keeps its provenance evidence\n * longest. Walks until either the pack fits or every page has zero\n * windows.\n */\nfunction trimSourceWindows(\n  pack: ContextPack,\n  budget: number,\n  trimmed: Set<TrimmedSection>,\n): void {\n  for (let i = pack.primary.length - 1; i >= 0; i--) {\n    while (pack.primary[i].sourceWindows.length > 0 && estimatePackTokens(pack) > budget) {\n      pack.primary[i].sourceWindows.pop();\n      trimmed.add(\"sourceWindows\");\n    }\n    if (estimatePackTokens(pack) <= budget) return;\n  }\n}\n\n/** Drop semantic chunks page-by-page using the same bottom-up strategy. */\nfunction trimChunks(\n  pack: ContextPack,\n  budget: number,\n  trimmed: Set<TrimmedSection>,\n): void {\n  for (let i = pack.primary.length - 1; i >= 0; i--) {\n    while (pack.primary[i].chunks.length > 0 && estimatePackTokens(pack) > budget) {\n      pack.primary[i].chunks.pop();\n      trimmed.add(\"chunks\");\n    }\n    if (estimatePackTokens(pack) <= budget) return;\n  }\n}\n\n/** Final resort: drop primary pages from the bottom of the ranked list. */\nfunction trimPrimary(\n  pack: ContextPack,\n  budget: number,\n  trimmed: Set<TrimmedSection>,\n): void {\n  while (pack.primary.length > 0 && estimatePackTokens(pack) > budget) {\n    pack.primary.pop();\n    trimmed.add(\"primary\");\n  }\n}\n","/**\n * Stable v1 JSON contract for `llmwiki context` and the future\n * `get_context_pack` MCP tool.\n *\n * Every top-level field and every documented nested key is present from\n * Slice 1 onward, even when later-slice features have not populated\n * them yet (see `localdocs/context-graph-packs-implementation-plan.md`\n * §JSON Contract). Unpopulated list fields are empty arrays; absent\n * object fields are `null`. Slices may fill data into these fields,\n * but must NEVER add or remove top-level keys without bumping\n * `version`.\n */\n\nimport type { PageId } from \"../viewer/types.js\";\nimport type { PageDirectory } from \"../export/types.js\";\nimport type { RecommendedAction } from \"../project/recommendations.js\";\nimport type { FreshnessStatus } from \"../freshness/types.js\";\n\n/** Closed v1 enum for why a page landed in `primary[]`. */\nexport type PrimaryReason =\n  | \"semantic-chunk\"\n  | \"title-match\"\n  | \"body-match\"\n  | \"exact-slug\"\n  | \"exact-title\"\n  | \"graph-neighbor\";\n\n/** Closed v1 enum for the edge label used in `neighbors[]`. */\ntype NeighborReason = \"wikilink\";\n\n/** Closed v1 enum for top-level `warnings[]` codes. */\ntype ContextWarningCode =\n  | \"embedding-store-missing\"\n  | \"query-embedding-unavailable\"\n  | \"semantic-retrieval-error\"\n  | \"lint-errors\"\n  | \"pending-candidates\"\n  | \"source-window-unavailable\"\n  | \"truncated-prompt\";\n\n/** Closed v1 enum for `gaps[]` codes. */\ntype ContextGapCode = \"dangling-link\" | \"page-warning\";\n\n/**\n * Budget envelope. `estimatedTokens` uses a tokens ≈ chars/4 heuristic in v1.\n * Because `estimatedTokens` is itself serialized inside the measured JSON, the\n * reported value may differ from `estimatePackTokens(returnedPack)` by at most\n * one token of digit-count drift.\n */\nexport interface ContextBudget {\n  requestedTokens: number;\n  estimatedTokens: number;\n  truncated: boolean;\n  /** Section keys (`primary`, `neighbors`, `sourceWindows`, `chunks`) that lost data. */\n  trimmedSections: string[];\n}\n\n/**\n * Cached lint summary surfaced inside `project.lint`. Matches\n * `LintCacheEntry` in `src/linter/cache.ts` but typed locally so the\n * context contract does not depend on the linter's internal shape.\n */\ninterface ContextLintSummary {\n  warnings: number;\n  errors: number;\n  at: string;\n}\n\n/** Project block. `root` is set to `null` when `--omit-root` is supplied. */\nexport interface ContextProject {\n  root: string | null;\n  pages: number;\n  pendingCandidates: number;\n  lint: ContextLintSummary | null;\n}\n\n/** One semantic chunk surfaced for a primary page. Slice 2 populates it. */\ninterface ContextChunk {\n  text: string;\n  score: number;\n  contentHash?: string;\n}\n\n/**\n * Flattened citation. Produced by lifting `ClaimCitation.spans` into one\n * object per span. Paragraph-only citations omit `start` and `end`.\n */\ninterface ContextCitation {\n  file: string;\n  start?: number;\n  end?: number;\n}\n\n/** Source line window emitted only when `--include-sources` is set in Slice 4. */\ninterface ContextSourceWindow {\n  file: string;\n  start: number;\n  end: number;\n  text: string;\n}\n\n/** Page-local warning surfaced from the viewer collector. */\ninterface ContextPageWarning {\n  code: string;\n  message: string;\n}\n\n/** One primary page entry. `reasons` is sorted alphabetically for stable output. */\nexport interface ContextPrimary {\n  id: PageId;\n  title: string;\n  pageDirectory: PageDirectory;\n  score: number;\n  reasons: PrimaryReason[];\n  summary: string;\n  chunks: ContextChunk[];\n  citations: ContextCitation[];\n  sourceWindows: ContextSourceWindow[];\n  warnings: ContextPageWarning[];\n  // The three freshness signals are FLATTENED here (rather than nested as a\n  // `freshness: PageFreshness` object like `ViewerPage`) for an idiomatic JSON\n  // wire shape for agents. Consequently, any future field added to\n  // `PageFreshness` must be mirrored here by hand — it won't auto-propagate.\n  /** Computed source-freshness of this page (advisory snapshot, not a guarantee). */\n  freshnessStatus: FreshnessStatus;\n  /** Disputed by another page (`contradictedBy` non-empty). */\n  contradicted: boolean;\n  /** Explicitly archived (`archived: true` frontmatter). */\n  archived: boolean;\n}\n\n/** One graph neighbor edge. `distance` is 1 for direct, 2 for second-hop. */\ninterface ContextNeighbor {\n  from: PageId;\n  to: PageId;\n  direction: \"outgoing\" | \"incoming\";\n  distance: number;\n  score: number;\n  reason: NeighborReason;\n}\n\n/** Top-level context-pack state warning. */\nexport interface ContextWarning {\n  code: ContextWarningCode;\n  message: string;\n}\n\n/**\n * Missing-knowledge gap. `pageId` is required in v1; every documented\n * gap code (`dangling-link`, `page-warning`) is tied to a specific\n * page. A future project-wide gap would either bump `version` or\n * introduce a new sibling field rather than retrofitting nullability\n * onto this one.\n */\ninterface ContextGap {\n  code: ContextGapCode;\n  message: string;\n  pageId: PageId;\n}\n\n/** Top-level v1 envelope. */\nexport interface ContextPack {\n  version: 1;\n  prompt: string;\n  budget: ContextBudget;\n  project: ContextProject;\n  primary: ContextPrimary[];\n  neighbors: ContextNeighbor[];\n  warnings: ContextWarning[];\n  gaps: ContextGap[];\n  suggestedActions: RecommendedAction[];\n}\n\n/** Hard cap on the echoed prompt; ranking still uses the original. */\nexport const PROMPT_ECHO_MAX_LENGTH = 1024;\n\n/** Default budget when `--budget` is omitted. */\nexport const DEFAULT_BUDGET_TOKENS = 8000;\n\n/** Default depth for graph expansion (1 = direct neighbors only). */\nexport const DEFAULT_DEPTH = 1;\n\n/** Hard upper bound on `--depth` per plan §Graph Expansion. */\nexport const MAX_DEPTH = 2;\n\n/** Default cap on `primary[]` page count. */\nexport const DEFAULT_TOP_PAGES = 5;\n\n/** Hard cap on `primary[]` page count to keep trimming and output bounded. */\nexport const MAX_TOP_PAGES = 20;\n\n/** Default value pinned for `--top-chunks` (plan §Ranking Model). */\nexport const DEFAULT_TOP_CHUNKS = 8;\n\n/** Hard cap on semantic chunks to keep budget trimming predictably small. */\nexport const MAX_TOP_CHUNKS = 50;\n","/**\n * `buildContextPack()` — Slice 1 orchestrator.\n *\n * Composes the v1 context-pack envelope by:\n *   1. Loading the frozen viewer snapshot (page metadata, frontmatter,\n *      citations, warnings, etc).\n *   2. Collecting project state via the shared `collectProjectState`\n *      helper so the lint cache and pending-candidate counts match\n *      what `llmwiki next` would report.\n *   3. Lexically ranking pages against the prompt via the Slice-1\n *      ranker.\n *   4. Delegating the recommendation prefix to\n *      `recommendNextAction(state)` so `context` does not introduce a\n *      second project-state engine.\n *\n * Semantic retrieval, graph expansion, source windows, and MCP are\n * intentionally left for later slices; this entry point already emits\n * the full stable v1 JSON field set with empty arrays / `null`\n * placeholders so agents written against Slice 1 will not break when\n * later slices add data.\n */\n\nimport { buildViewerSnapshot } from \"../viewer/snapshot.js\";\nimport { collectProjectState } from \"../project/state.js\";\nimport { recommendNextAction } from \"../project/recommendations.js\";\nimport type { Recommendation, RecommendedAction } from \"../project/recommendations.js\";\nimport type { ProjectState } from \"../project/state.js\";\nimport type { ViewerSnapshot } from \"../viewer/types.js\";\nimport { rankPages } from \"./ranking.js\";\nimport { retrieveSemanticChunks } from \"./retrieval.js\";\nimport type { SemanticRetrievalOutcome, SemanticRetrievalWarning } from \"./retrieval.js\";\nimport { expandGraphNeighborhood } from \"./graph.js\";\nimport type { GraphExpansionOutput } from \"./graph.js\";\nimport {\n  createSourceWindowBudget,\n  materializeSourceWindows,\n} from \"./provenance.js\";\nimport type { GraphData, PageId } from \"../viewer/types.js\";\nimport { buildBudget, estimatePackTokens, trimToBudget } from \"./budget.js\";\nimport {\n  DEFAULT_BUDGET_TOKENS,\n  DEFAULT_DEPTH,\n  DEFAULT_TOP_CHUNKS,\n  DEFAULT_TOP_PAGES,\n  MAX_DEPTH,\n  MAX_TOP_CHUNKS,\n  MAX_TOP_PAGES,\n  PROMPT_ECHO_MAX_LENGTH,\n} from \"./types.js\";\nimport type {\n  ContextPack,\n  ContextProject,\n  ContextWarning,\n} from \"./types.js\";\n\n/** Caller-supplied build options; all fields except `prompt` are optional. */\ninterface BuildContextPackOptions {\n  /** Project root; defaults to `process.cwd()` at the call site. */\n  root: string;\n  /** Free-text prompt the agent supplied. */\n  prompt: string;\n  /** Token budget; defaults to {@link DEFAULT_BUDGET_TOKENS}. */\n  budget?: number;\n  /** Graph depth; clamped to {@link MAX_DEPTH} when supplied. */\n  depth?: number;\n  /** Max primary pages; clamped into the documented safe range. */\n  topPages?: number;\n  /** Max semantic chunks; pinned to the documented safe range. */\n  topChunks?: number;\n  /** When true, `project.root` is emitted as `null` for privacy. */\n  omitRoot?: boolean;\n  /** When false, graph expansion is suppressed (neighbors + gaps stay empty). */\n  neighbors?: boolean;\n  /** When true, populate `primary[].sourceWindows` from claim-level citation spans. */\n  includeSources?: boolean;\n}\n\n/**\n * Build the v1 context pack. Never throws on read-only filesystem\n * issues — the project-state collector returns conservative defaults\n * (`broken-project` state) which the orchestrator faithfully surfaces.\n */\nexport async function buildContextPack(options: BuildContextPackOptions): Promise<ContextPack> {\n  const normalized = normalizeOptions(options);\n  const snapshot = await buildViewerSnapshot(options.root);\n  const state = await collectProjectState(options.root);\n  const recommendation = recommendNextAction(state);\n  // Semantic retrieval is opportunistic — failures surface as stable\n  // warning codes on the returned outcome rather than thrown errors so\n  // lexical-only flows stay the default behaviour for credential-free\n  // users.\n  const semantic = await retrieveSemanticChunks(\n    options.root,\n    normalized.rankingPrompt,\n    normalized.topChunks,\n  );\n  const draft = assembleDraft({\n    snapshot,\n    state,\n    recommendation,\n    options: normalized,\n    semantic,\n  });\n  // Source windows are materialized AFTER ranking so the per-pack\n  // budget sees the final primary list, not every candidate.\n  // Skipped entirely when `--include-sources` is off.\n  const withSources = normalized.includeSources\n    ? await attachSourceWindows(draft, options.root)\n    : draft;\n  // Project-state warnings (pending candidates, lint errors,\n  // source-window unavailability) need the post-materialization\n  // primary list, so they land after attachSourceWindows and BEFORE\n  // budget trimming. Trimming may drop sourceWindows for budget\n  // reasons; the warning still correctly reports \"windows missing\".\n  const withProjectWarnings = appendProjectWarnings(withSources, state, normalized);\n  const graph = normalized.neighborsEnabled && normalized.depth >= 1\n    ? snapshot.graph\n    : null;\n  return finalizeBudget(withProjectWarnings, normalized.budget, graph);\n}\n\n/**\n * Walk the ranked primary list once with a shared\n * {@link createSourceWindowBudget}, filling in each entry's\n * `sourceWindows` from its (already-flattened) claim-level citations.\n * Pages without claim-level spans (paragraph-only or no citations)\n * return empty windows; the global 20-window cap is enforced as the\n * walk progresses.\n */\nasync function attachSourceWindows(pack: ContextPack, root: string): Promise<ContextPack> {\n  const budget = createSourceWindowBudget();\n  // Serial loop — `budget.remaining` is mutated between awaits inside\n  // `materializeSourceWindows`, so running pages in parallel would\n  // race on the shared counter and overshoot the 20-window cap.\n  const primary: ContextPack[\"primary\"] = [];\n  for (const entry of pack.primary) {\n    const windows = await materializeSourceWindows(root, entry.citations, budget);\n    primary.push({ ...entry, sourceWindows: windows });\n  }\n  return { ...pack, primary };\n}\n\n/**\n * Frozen, validated copy of the user-supplied options.\n *\n * The prompt is intentionally split into two fields:\n *   - `displayPrompt` is the echo-safe form that lands in\n *     `ContextPack.prompt` (truncated at PROMPT_ECHO_MAX_LENGTH so the\n *     envelope cannot balloon on a 10KB agent input).\n *   - `rankingPrompt` is the original, untruncated prompt that flows\n *     into every retrieval signal — lexical, semantic (Slice 2+), and\n *     exact match. Truncating before ranking would silently drop\n *     content the agent expected to drive selection.\n *\n * In Slice 1 the two values are observationally equivalent at the\n * lexical layer because `searchPages` caps queries at its own internal\n * MAX_QUERY_LENGTH (200 chars) and exact-match requires whole-prompt\n * equality. Slice 2's semantic retrieval will see the full\n * `rankingPrompt` and produce different scores than it would against\n * `displayPrompt`.\n */\ninterface NormalizedOptions {\n  displayPrompt: string;\n  rankingPrompt: string;\n  budget: number;\n  depth: number;\n  topPages: number;\n  topChunks: number;\n  omitRoot: boolean;\n  neighborsEnabled: boolean;\n  includeSources: boolean;\n  promptTruncated: boolean;\n}\n\n/** Apply defaults and clamps so downstream code can trust the field types. */\nfunction normalizeOptions(options: BuildContextPackOptions): NormalizedOptions {\n  const rankingPrompt = options.prompt ?? \"\";\n  const { display, truncated } = truncatePrompt(rankingPrompt);\n  return {\n    displayPrompt: display,\n    rankingPrompt,\n    budget: clampPositive(options.budget, DEFAULT_BUDGET_TOKENS),\n    depth: clampDepth(options.depth),\n    topPages: clampBounded(options.topPages, DEFAULT_TOP_PAGES, MAX_TOP_PAGES),\n    topChunks: clampBounded(options.topChunks, DEFAULT_TOP_CHUNKS, MAX_TOP_CHUNKS),\n    omitRoot: options.omitRoot === true,\n    // `--no-neighbors` is a Commander negated flag: absence means\n    // expansion is ON; only `options.neighbors === false` disables it.\n    neighborsEnabled: options.neighbors !== false,\n    includeSources: options.includeSources === true,\n    promptTruncated: truncated,\n  };\n}\n\n/** Truncate the echoed prompt without mutating the prompt used for ranking. */\nfunction truncatePrompt(raw: string): { display: string; truncated: boolean } {\n  if (raw.length <= PROMPT_ECHO_MAX_LENGTH) return { display: raw, truncated: false };\n  return { display: raw.slice(0, PROMPT_ECHO_MAX_LENGTH), truncated: true };\n}\n\n/** Clamp a numeric option to a non-negative integer with a fallback default. */\nfunction clampPositive(value: number | undefined, fallback: number): number {\n  if (value === undefined || !Number.isFinite(value)) return fallback;\n  return Math.max(0, Math.floor(value));\n}\n\n/** Clamp a numeric option into `[0, max]` with a fallback default. */\nfunction clampBounded(value: number | undefined, fallback: number, max: number): number {\n  return Math.min(max, clampPositive(value, fallback));\n}\n\n/** Clamp `--depth` into `[0, MAX_DEPTH]`. */\nfunction clampDepth(value: number | undefined): number {\n  if (value === undefined || !Number.isFinite(value)) return DEFAULT_DEPTH;\n  return Math.max(0, Math.min(MAX_DEPTH, Math.floor(value)));\n}\n\n/** Composite input passed to the assembler; grouped to keep argument lists short. */\ninterface AssembleInput {\n  snapshot: ViewerSnapshot;\n  state: ProjectState;\n  recommendation: Recommendation;\n  options: NormalizedOptions;\n  semantic: SemanticRetrievalOutcome;\n}\n\n/** Build the unbudgeted draft pack before token-budget finalization. */\nfunction assembleDraft(input: AssembleInput): ContextPack {\n  const { snapshot, state, recommendation, options, semantic } = input;\n  const project = buildProject(snapshot, state, options.omitRoot);\n  // Rank against the ORIGINAL prompt — the truncated echo is a\n  // display-only courtesy and must not silently drop ranking signal.\n  const primary = rankPages(snapshot, options.rankingPrompt, options.topPages, semantic.hits);\n  const graphEnabled = options.neighborsEnabled && options.depth >= 1;\n  const expansion = graphEnabled\n    ? expandGraphNeighborhood({\n        graph: snapshot.graph,\n        pages: snapshot.pages,\n        primaryIds: collectPrimaryIds(primary),\n        depth: options.depth,\n      })\n    : emptyExpansion();\n  // Additive `graph-neighbor` reason only: cannot promote a page into\n  // primary[], only annotate entries that earned their slot via\n  // semantic/lexical/exact signals AND link to another primary page.\n  // Gated on `graphEnabled` so `--no-neighbors` / `--depth 0` runs\n  // never surface the reason (no graph context to justify it).\n  const annotatedPrimary = graphEnabled\n    ? annotateGraphNeighbors(primary, snapshot.graph)\n    : primary;\n  return {\n    version: 1,\n    prompt: options.displayPrompt,\n    budget: buildBudget(options.budget, 0),\n    project,\n    primary: annotatedPrimary,\n    neighbors: expansion.neighbors,\n    warnings: buildTopLevelWarnings(options.promptTruncated, semantic.warning),\n    gaps: expansion.gaps,\n    suggestedActions: collectSuggestedActions(recommendation, {\n      hasPages: snapshot.pages.length > 0,\n      semanticWarning: semantic.warning,\n    }),\n  };\n}\n\n/**\n * Append `graph-neighbor` to existing primary entries that have a\n * wikilink edge (outgoing OR incoming) to another primary entry. Pure:\n * never reorders, rescores, or admits new entries — only widens the\n * `reasons[]` set on entries that already passed ranking. Reasons stay\n * sorted alphabetically and de-duped so snapshot comparisons remain\n * stable.\n */\nfunction annotateGraphNeighbors(\n  primary: ContextPack[\"primary\"],\n  graph: GraphData,\n): ContextPack[\"primary\"] {\n  if (primary.length < 2) return primary;\n  const primaryIds = collectPrimaryIds(primary);\n  const connected = new Set<PageId>();\n  for (const edge of graph.edges) {\n    if (primaryIds.has(edge.source) && primaryIds.has(edge.target)) {\n      connected.add(edge.source);\n      connected.add(edge.target);\n    }\n  }\n  if (connected.size === 0) return primary;\n  return primary.map((entry) => {\n    if (!connected.has(entry.id)) return entry;\n    if (entry.reasons.includes(\"graph-neighbor\")) return entry;\n    const widened = Array.from(new Set([...entry.reasons, \"graph-neighbor\" as const])).sort();\n    return { ...entry, reasons: widened };\n  });\n}\n\n/** Collapse the ranked primary list into a Set keyed by PageId for fast lookups. */\nfunction collectPrimaryIds(primary: ContextPack[\"primary\"]): Set<PageId> {\n  const ids = new Set<PageId>();\n  for (const entry of primary) ids.add(entry.id);\n  return ids;\n}\n\n/** Strip graph-derived reasons so they can be recomputed after budget trimming. */\nfunction stripGraphNeighborReason(\n  primary: ContextPack[\"primary\"],\n): ContextPack[\"primary\"] {\n  return primary.map((entry) => ({\n    ...entry,\n    reasons: entry.reasons.filter((reason) => reason !== \"graph-neighbor\"),\n  }));\n}\n\n/** Reconcile graph-neighbor after trimToBudget may have removed a connected peer. */\nfunction reconcileGraphNeighborReasons(\n  pack: ContextPack,\n  graph: GraphData | null,\n): ContextPack {\n  const stripped = stripGraphNeighborReason(pack.primary);\n  const primary = graph ? annotateGraphNeighbors(stripped, graph) : stripped;\n  return primary === pack.primary ? pack : { ...pack, primary };\n}\n\n/** Empty expansion used when `--no-neighbors` suppresses graph traversal. */\nfunction emptyExpansion(): GraphExpansionOutput {\n  return { neighbors: [], gaps: [] };\n}\n\n/** Materialize the `project` block; `root` honors the `--omit-root` flag. */\nfunction buildProject(\n  snapshot: ViewerSnapshot,\n  state: ProjectState,\n  omitRoot: boolean,\n): ContextProject {\n  return {\n    root: omitRoot ? null : snapshot.root,\n    pages: snapshot.pages.length,\n    pendingCandidates: state.pendingCandidates,\n    lint: state.lint.entry,\n  };\n}\n\n/**\n * Top-level state warnings. Slice 1 wired `truncated-prompt`; Slice 2\n * adds the two semantic-retrieval fallback codes so consumers can tell\n * \"lexical-only because no embeddings on disk\" apart from \"lexical-only\n * because the provider rejected our embed call.\"\n */\nfunction buildTopLevelWarnings(\n  promptTruncated: boolean,\n  retrievalWarning: SemanticRetrievalWarning | null,\n): ContextWarning[] {\n  const warnings: ContextWarning[] = [];\n  if (promptTruncated) {\n    warnings.push({\n      code: \"truncated-prompt\",\n      message: `Prompt exceeded ${PROMPT_ECHO_MAX_LENGTH} characters; the echoed copy was truncated.`,\n    });\n  }\n  if (retrievalWarning === \"embedding-store-missing\") {\n    warnings.push({\n      code: \"embedding-store-missing\",\n      message:\n        \"No usable embedding store found; semantic retrieval skipped. \" +\n        \"Run `llmwiki compile` to populate embeddings.\",\n    });\n  } else if (retrievalWarning === \"query-embedding-unavailable\") {\n    warnings.push({\n      code: \"query-embedding-unavailable\",\n      message:\n        \"Could not embed the prompt with the active provider; \" +\n        \"semantic retrieval skipped, lexical signals still applied.\",\n    });\n  } else if (retrievalWarning === \"semantic-retrieval-error\") {\n    warnings.push({\n      code: \"semantic-retrieval-error\",\n      message:\n        \"Semantic retrieval failed unexpectedly; \" +\n        \"lexical signals still applied and raw provider errors were not exposed.\",\n    });\n  }\n  return warnings;\n}\n\n/**\n * Flatten the recommendation engine's output into the array-shaped\n * `suggestedActions[]`. Per plan §Suggested Actions:\n *   - index 0 is the primary recommendation\n *   - subsequent entries are `otherActions` in declared order\n *   - tests pin the prefix only; context-specific additions land in\n *     later slices.\n */\ninterface ContextActionInput {\n  hasPages: boolean;\n  semanticWarning: SemanticRetrievalWarning | null;\n}\n\n/** Context-specific suffix: rebuild embeddings when pages exist but no store is usable. */\nconst CONTEXT_COMPILE_ACTION: RecommendedAction = {\n  command: \"llmwiki compile\",\n  reason: \"Refresh compiled pages and rebuild the embedding store for semantic context.\",\n  executable: { binary: \"llmwiki\", args: [\"compile\"] },\n};\n\n/** Context-specific suffix: open the selected wiki when shared recommendations omit it. */\nconst CONTEXT_VIEW_ACTION: RecommendedAction = {\n  command: \"llmwiki view --open\",\n  reason: \"Browse the compiled wiki in the local viewer.\",\n  executable: { binary: \"llmwiki\", args: [\"view\", \"--open\"] },\n};\n\n/** Context-specific suffix: use the same prompt to generate an answer after reviewing evidence. */\nconst CONTEXT_QUERY_ACTION: RecommendedAction = {\n  command: 'llmwiki query \"<prompt>\"',\n  reason: \"Generate an answer with the same prompt after reviewing this context pack.\",\n  executable: { binary: \"llmwiki\", args: [\"query\"], placeholders: [\"prompt\"] },\n};\n\nfunction collectSuggestedActions(\n  recommendation: Recommendation,\n  input: ContextActionInput,\n): RecommendedAction[] {\n  const actions: RecommendedAction[] = [];\n  for (const action of [recommendation.recommended, ...recommendation.otherActions]) {\n    appendUniqueAction(actions, action);\n  }\n  if (input.hasPages && input.semanticWarning === \"embedding-store-missing\") {\n    appendUniqueAction(actions, CONTEXT_COMPILE_ACTION);\n  }\n  if (input.hasPages) {\n    appendUniqueAction(actions, CONTEXT_VIEW_ACTION);\n    appendUniqueAction(actions, CONTEXT_QUERY_ACTION);\n  }\n  return actions;\n}\n\n/** Add `candidate` unless an equivalent executable action is already present. */\nfunction appendUniqueAction(actions: RecommendedAction[], candidate: RecommendedAction): void {\n  if (actions.some((action) => actionKey(action) === actionKey(candidate))) return;\n  actions.push(candidate);\n}\n\n/** Dedupe by executable intent, falling back to display command for non-executable actions. */\nfunction actionKey(action: RecommendedAction): string {\n  if (!action.executable) return action.command ?? action.reason;\n  return `${action.executable.binary} ${action.executable.args.join(\" \")}`;\n}\n\n/**\n * Compute `budget.estimatedTokens` from the serialized draft and\n * trim down the lower-priority sections deterministically when the\n * draft overshoots `requestedTokens`. See `src/context/budget.ts`\n * for the trim order. Always emits valid JSON; the structured\n * envelope is mutated section-by-section rather than slicing the\n * serialized string.\n *\n * `budget.truncated` is `true` when EITHER any section was trimmed\n * OR the final estimated envelope still exceeds `requestedTokens`\n * (irreducible-envelope edge case: empty wiki + very small budget).\n * In the latter case `trimmedSections` stays `[]` — the closed\n * section-key contract is not bent to record \"nothing was trimmable\".\n *\n * `budget.estimatedTokens` is recomputed against the FINAL envelope\n * shape (post-trim, post-truncated-flag, post-trimmedSections) via a\n * two-pass estimate that converges on the digit-count fixed point of\n * `estimatedTokens` itself. The residual drift between the reported\n * `estimatedTokens` and `estimatePackTokens(returnedPack)` is bounded\n * to a single character of the integer's decimal representation —\n * well under one token for any realistic budget.\n */\nfunction finalizeBudget(\n  draft: ContextPack,\n  requestedTokens: number,\n  graph: GraphData | null = null,\n): ContextPack {\n  const initialEstimate = estimatePackTokens(draft);\n  const trim = initialEstimate <= requestedTokens\n    ? { pack: draft, trimmedSections: [] as string[] }\n    : trimToBudget(draft, requestedTokens);\n  const trimmedAny = trim.trimmedSections.length > 0;\n  const reconciledPack = reconcileGraphNeighborReasons(trim.pack, graph);\n  // First pass: write the eventual `truncated`/`trimmedSections`\n  // strings into the budget block with a placeholder zero estimate so\n  // the JSON shape the estimator sees matches what we'll ultimately\n  // ship. Second pass: write the first estimate back and re-measure\n  // so the reported value converges on the digit-count fixed point.\n  const e1 = estimatePackTokens(\n    applyBudget(reconciledPack, {\n      requestedTokens, estimatedTokens: 0,\n      truncated: trimmedAny, trimmedSections: trim.trimmedSections,\n    }),\n  );\n  const e2 = estimatePackTokens(\n    applyBudget(reconciledPack, {\n      requestedTokens, estimatedTokens: e1,\n      truncated: trimmedAny, trimmedSections: trim.trimmedSections,\n    }),\n  );\n  const truncated = trimmedAny || e2 > requestedTokens;\n  return applyBudget(reconciledPack, {\n    requestedTokens,\n    estimatedTokens: e2,\n    truncated,\n    trimmedSections: trim.trimmedSections,\n  });\n}\n\n/** Replace `pack.budget` with `budget`, returning a fresh shallow-cloned envelope. */\nfunction applyBudget(pack: ContextPack, budget: ContextPack[\"budget\"]): ContextPack {\n  return { ...pack, budget };\n}\n\n/**\n * Append `pending-candidates`, `lint-errors`, and\n * `source-window-unavailable` to the top-level warnings list.\n *\n * Runs AFTER source-window materialization so we can detect the gap\n * where `--include-sources` was on but a line-range citation\n * produced no window (path-confined rejection, missing source file,\n * 20-window cap reached, …). Runs BEFORE budget trimming so a\n * budget-induced window drop does NOT spuriously add the warning;\n * the trimmer mutates sourceWindows only after this pass.\n */\nfunction appendProjectWarnings(\n  pack: ContextPack,\n  state: ProjectState,\n  options: NormalizedOptions,\n): ContextPack {\n  const warnings = [...pack.warnings];\n  if (state.pendingCandidates > 0) {\n    warnings.push({\n      code: \"pending-candidates\",\n      message:\n        `${state.pendingCandidates} review candidate${state.pendingCandidates === 1 ? \"\" : \"s\"} ` +\n        \"pending approval. Run `llmwiki review list` to inspect.\",\n    });\n  }\n  const lintErrors = state.lint.entry?.errors ?? 0;\n  if (lintErrors > 0) {\n    warnings.push({\n      code: \"lint-errors\",\n      message: `Last lint run reported ${lintErrors} error${lintErrors === 1 ? \"\" : \"s\"}.`,\n    });\n  }\n  if (options.includeSources && hasUnmaterializedSpans(pack)) {\n    warnings.push({\n      code: \"source-window-unavailable\",\n      message:\n        \"One or more line-range citations did not produce a source window \" +\n        \"(path-confined, missing source file, or per-pack window cap reached).\",\n    });\n  }\n  return { ...pack, warnings };\n}\n\n/** True when any primary page has line-range citations missing matching sourceWindows. */\nfunction hasUnmaterializedSpans(pack: ContextPack): boolean {\n  for (const entry of pack.primary) {\n    const lineRangeCount = entry.citations.filter(\n      (c) => c.start !== undefined && c.end !== undefined,\n    ).length;\n    if (lineRangeCount > entry.sourceWindows.length) return true;\n  }\n  return false;\n}\n","/**\n * Commander action for `llmwiki export [--target <name>]`.\n *\n * Transforms existing wiki content into portable export artifacts and writes\n * them into dist/exports/ (relative to the project root). Supports six formats:\n *\n *   llms-txt      — concise index per llmstxt.org spec → llms.txt\n *   llms-full-txt — full content export               → llms-full.txt\n *   json          — pages + metadata as JSON          → wiki.json\n *   json-ld       — Schema.org JSON-LD graph          → wiki.jsonld\n *   graphml       — directed link graph as XML        → wiki.graphml\n *   marp          — Marp slide deck                   → wiki.md\n *\n * No LLM calls are made — export is a pure transformation of wiki content.\n */\n\nimport path from \"path\";\nimport { createRequire } from \"module\";\nimport { atomicWrite } from \"../utils/markdown.js\";\nimport * as output from \"../utils/output.js\";\nimport { collectExportPages } from \"../export/collect.js\";\nimport { buildLlmsTxt, buildLlmsFullTxt } from \"../export/llms-txt.js\";\nimport {\n  buildJsonExport,\n  buildJsonExportDocument,\n  type BuildJsonExportOptions,\n  type JsonExportDocument,\n} from \"../export/json-export.js\";\nimport { validateProjectId } from \"../export/project-id.js\";\nimport { buildJsonLd } from \"../export/json-ld.js\";\nimport { buildGraphml } from \"../export/graphml.js\";\nimport { buildMarp } from \"../export/marp.js\";\nimport { EXPORT_TARGETS, MARP_SOURCES } from \"../export/types.js\";\nimport type { ExportPage, ExportTarget, MarpSource } from \"../export/types.js\";\n\nconst require = createRequire(import.meta.url);\n\n/** Output paths relative to dist/exports/ within the project root. */\nconst EXPORT_DIR = \"dist/exports\";\n\n/** Map each target to its output filename. */\nconst TARGET_FILENAMES: Record<ExportTarget, string> = {\n  \"llms-txt\": \"llms.txt\",\n  \"llms-full-txt\": \"llms-full.txt\",\n  json: \"wiki.json\",\n  \"json-ld\": \"wiki.jsonld\",\n  graphml: \"wiki.graphml\",\n  marp: \"wiki.md\",\n};\n\n/** Options accepted by exportCommand and its programmatic entry point. */\nexport interface ExportOptions {\n  /** Limit export to a single target. When absent all targets are produced. */\n  target?: string;\n  /**\n   * For the marp target: which page kinds to include.\n   * Accepts \"concepts\", \"queries\", or \"all\" (default when absent).\n   */\n  source?: string;\n  /**\n   * Optional bridge identifier embedded in the JSON export envelope.\n   * Validated against the bridge contract regex\n   * (`/^[a-z0-9][a-z0-9-]{0,62}$/`); invalid values throw before any\n   * file is written.\n   */\n  projectId?: string;\n}\n\n/** Result returned by runExport for testing and MCP consumers. */\nexport interface ExportResult {\n  /** Absolute paths of files that were written. */\n  written: string[];\n  /** Number of pages included in each export. */\n  pageCount: number;\n}\n\n/** Resolve the human-readable project title from package.json, defaulting gracefully. */\nfunction resolveProjectTitle(root: string): string {\n  try {\n    const pkg = require(path.join(root, \"package.json\")) as { name?: string };\n    return typeof pkg.name === \"string\" ? pkg.name : \"Knowledge Wiki\";\n  } catch {\n    return \"Knowledge Wiki\";\n  }\n}\n\n/** Return true when the given string is a valid ExportTarget. */\nfunction isValidTarget(value: string): value is ExportTarget {\n  return (EXPORT_TARGETS as readonly string[]).includes(value);\n}\n\n/** Return true when the given string is a valid MarpSource. */\nfunction isValidMarpSource(value: string): value is MarpSource {\n  return (MARP_SOURCES as readonly string[]).includes(value);\n}\n\n/** Resolve and validate the marp source filter. Throws for unknown values. */\nfunction resolveMarpSource(rawSource: string | undefined): MarpSource {\n  if (!rawSource) return \"all\";\n  if (!isValidMarpSource(rawSource)) {\n    throw new Error(\n      `Unknown --source value \"${rawSource}\". Valid values: ${MARP_SOURCES.join(\", \")}`,\n    );\n  }\n  return rawSource;\n}\n\n/** Inputs to {@link buildContent}. Grouped to keep the argument list short. */\ninterface BuildContentInputs {\n  target: ExportTarget;\n  pages: ExportPage[];\n  projectTitle: string;\n  marpSource: MarpSource;\n  /** Optional bridge identifier; only consumed by the json target. */\n  projectId?: string;\n}\n\n/** Build the content string for a single target. */\nfunction buildContent(inputs: BuildContentInputs): string {\n  const { target, pages, projectTitle, marpSource, projectId } = inputs;\n  switch (target) {\n    case \"llms-txt\":\n      return buildLlmsTxt(pages, projectTitle);\n    case \"llms-full-txt\":\n      return buildLlmsFullTxt(pages, projectTitle);\n    case \"json\":\n      return buildJsonExport(pages, projectId !== undefined ? { projectId } : {});\n    case \"json-ld\":\n      return buildJsonLd(pages);\n    case \"graphml\":\n      return buildGraphml(pages);\n    case \"marp\":\n      return buildMarp(pages, projectTitle, marpSource);\n  }\n}\n\n/**\n * Compute the page count to report in the CLI summary. When marp is the\n * only target and --source narrows the deck, report the filtered count so\n * the summary doesn't overstate what was exported. Multi-target runs keep\n * the collected total because non-marp targets always include every page.\n */\nfunction computeReportedPageCount(\n  pages: ExportPage[],\n  targets: ExportTarget[],\n  marpSource: MarpSource,\n): number {\n  const onlyMarpTarget = targets.length === 1 && targets[0] === \"marp\";\n  if (onlyMarpTarget && marpSource !== \"all\") {\n    return pages.filter((p) => p.pageDirectory === marpSource).length;\n  }\n  return pages.length;\n}\n\n/**\n * Programmatic entry point for the export pipeline.\n * @param root - Absolute path to the project root directory.\n * @param options - Export options (optional target filter).\n * @returns Paths written and page count.\n */\nexport async function runExport(root: string, options: ExportOptions = {}): Promise<ExportResult> {\n  const projectId =\n    options.projectId !== undefined ? validateProjectId(options.projectId) : undefined;\n  const pages = await collectExportPages(root);\n  const projectTitle = resolveProjectTitle(root);\n\n  const targets = resolveTargets(options.target);\n  const marpSource = resolveMarpSource(options.source);\n  const written: string[] = [];\n\n  for (const target of targets) {\n    const content = buildContent({ target, pages, projectTitle, marpSource, projectId });\n    const outPath = path.join(root, EXPORT_DIR, TARGET_FILENAMES[target]);\n    await atomicWrite(outPath, content);\n    written.push(outPath);\n    output.status(\"+\", output.success(`Exported ${target} → ${output.source(outPath)}`));\n  }\n\n  return { written, pageCount: computeReportedPageCount(pages, targets, marpSource) };\n}\n\n/**\n * Resolve the list of targets to run.\n * When a specific target is given it is validated; an error is thrown for unknown values.\n * Defaults to all targets.\n */\nfunction resolveTargets(rawTarget: string | undefined): ExportTarget[] {\n  if (!rawTarget) return [...EXPORT_TARGETS];\n\n  if (!isValidTarget(rawTarget)) {\n    throw new Error(\n      `Unknown export target \"${rawTarget}\". Valid targets: ${EXPORT_TARGETS.join(\", \")}`,\n    );\n  }\n\n  return [rawTarget];\n}\n\n/**\n * Pure in-memory entry point — collects pages and returns the export document\n * object without writing any files or emitting console output.\n * @param root - Absolute path to the project root directory.\n * @param options - Optional export options (e.g. `projectId`).\n * @returns The JsonExportDocument object ready for programmatic consumption.\n */\nexport async function exportJson(\n  root: string,\n  options: BuildJsonExportOptions = {},\n): Promise<JsonExportDocument> {\n  const pages = await collectExportPages(root);\n  return buildJsonExportDocument(pages, options);\n}\n\n/**\n * CLI action for `llmwiki export`.\n * @param root - Project root directory (defaults to cwd).\n * @param options - Commander-parsed options.\n */\nexport default async function exportCommand(\n  root: string,\n  options: ExportOptions,\n): Promise<void> {\n  output.header(\"Exporting wiki\");\n  const { written, pageCount } = await runExport(root, options);\n  output.status(\n    \"✓\",\n    output.success(`Done — ${pageCount} pages exported to ${written.length} file(s).`),\n  );\n}\n","/**\n * Wiki page collector for the export subsystem.\n *\n * Thin wrapper over `src/wiki/collect.ts::collectRawWikiPages()` that\n * applies export-specific filters (drop orphaned and untitled pages) and\n * decorates each surviving record with the export-facing fields (summary,\n * sources, tags, timestamps, link slugs). The wikilink extraction regex\n * and slug-normalization helper live in `src/wiki/collect.ts` so both\n * export and viewer callers share one source.\n */\n\nimport path from \"path\";\nimport { collectRawWikiPages, extractWikilinkSlugs } from \"../wiki/collect.js\";\nimport type { RawWikiPage } from \"../wiki/collect.js\";\nimport { buildFreshnessSnapshot, computeFreshness } from \"../freshness/index.js\";\nimport type { FreshnessSnapshot } from \"../freshness/types.js\";\nimport { extractClaimCitations } from \"../utils/markdown.js\";\nimport { flattenCitations } from \"../context/provenance.js\";\nimport type { PageKind } from \"../schema/types.js\";\nimport type { ProvenanceState, ContradictionRef } from \"../utils/types.js\";\nimport { CONCEPTS_DIR, QUERIES_DIR } from \"../utils/constants.js\";\nimport {\n  hashPageBody,\n  resolveSourceHashes,\n  sourceHashLookupFromSnapshot,\n  type SourceHashLookup,\n} from \"./provenance.js\";\nimport type { ExportPage, PageDirectory } from \"./types.js\";\n\nexport { extractWikilinkSlugs };\n\n/** Resolve the project-relative path for a wiki page (e.g. `wiki/concepts/retrieval.md`). */\nfunction buildPagePath(pageDirectory: PageDirectory, slug: string): string {\n  const dir = pageDirectory === \"concepts\" ? CONCEPTS_DIR : QUERIES_DIR;\n  return path.posix.join(dir, `${slug}.md`);\n}\n\n/** Pull a typed string array out of frontmatter or return `[]` for missing/malformed input. */\nfunction readStringArray(meta: Record<string, unknown>, field: string): string[] {\n  const value = meta[field];\n  if (!Array.isArray(value)) return [];\n  return (value as unknown[]).filter((s): s is string => typeof s === \"string\");\n}\n\n/** Read a numeric confidence value if present and in the [0, 1] range. */\nfunction readAdvisoryConfidence(meta: Record<string, unknown>): number | undefined {\n  const value = meta.confidence;\n  if (typeof value !== \"number\" || !Number.isFinite(value)) return undefined;\n  if (value < 0 || value > 1) return undefined;\n  return value;\n}\n\n/** Validate and return a ProvenanceState from frontmatter, or undefined. */\nfunction readProvenanceState(meta: Record<string, unknown>): ProvenanceState | undefined {\n  const value = meta.provenanceState;\n  if (value === \"extracted\" || value === \"merged\" || value === \"inferred\" || value === \"ambiguous\") {\n    return value;\n  }\n  return undefined;\n}\n\n/** Filter ContradictionRef entries to the documented `{ slug, reason? }` shape. */\nfunction readContradictedBy(meta: Record<string, unknown>): ContradictionRef[] | undefined {\n  const raw = meta.contradictedBy;\n  if (!Array.isArray(raw)) return undefined;\n  const refs: ContradictionRef[] = [];\n  for (const entry of raw) {\n    if (!entry || typeof entry !== \"object\") continue;\n    const candidate = entry as Record<string, unknown>;\n    if (typeof candidate.slug !== \"string\" || candidate.slug.length === 0) continue;\n    const ref: ContradictionRef = { slug: candidate.slug };\n    if (typeof candidate.reason === \"string\") ref.reason = candidate.reason;\n    refs.push(ref);\n  }\n  return refs.length > 0 ? refs : undefined;\n}\n\n/** Validate and return PageKind from frontmatter, or undefined. */\nfunction readPageKind(meta: Record<string, unknown>): PageKind | undefined {\n  const value = meta.kind;\n  if (value === \"concept\" || value === \"entity\" || value === \"comparison\" || value === \"overview\") {\n    return value;\n  }\n  return undefined;\n}\n\n/**\n * Normalize a kept page into the shape every export writer consumes.\n * Caller is responsible for filtering out records that fail the export\n * gate (orphaned, untitled, unreadable). The bridge contract additions\n * (path, kind, advisory*, citations, aliases) are populated here so\n * every export format gets the same enriched payload.\n */\nfunction toExportPage(\n  raw: RawWikiPage,\n  snapshot: FreshnessSnapshot,\n  sourceHashes: SourceHashLookup,\n): ExportPage {\n  const meta = raw.frontmatter;\n  const aliases = readStringArray(meta, \"aliases\");\n  const sources = readStringArray(meta, \"sources\");\n  const freshness = computeFreshness(\n    { slug: raw.slug, pageDirectory: raw.pageDirectory, frontmatter: meta },\n    snapshot,\n  );\n  return {\n    title: raw.title as string,\n    slug: raw.slug,\n    pageDirectory: raw.pageDirectory,\n    path: buildPagePath(raw.pageDirectory, raw.slug),\n    summary: typeof meta.summary === \"string\" ? meta.summary : \"\",\n    sources,\n    tags: readStringArray(meta, \"tags\"),\n    createdAt: typeof meta.createdAt === \"string\" ? meta.createdAt : new Date().toISOString(),\n    updatedAt: typeof meta.updatedAt === \"string\" ? meta.updatedAt : new Date().toISOString(),\n    links: extractWikilinkSlugs(raw.body),\n    body: raw.body,\n    kind: readPageKind(meta),\n    advisoryConfidence: readAdvisoryConfidence(meta),\n    provenanceState: readProvenanceState(meta),\n    contradictedBy: readContradictedBy(meta),\n    citations: flattenCitations(extractClaimCitations(raw.body)),\n    ...(aliases.length > 0 ? { aliases } : {}),\n    freshnessStatus: freshness.freshnessStatus,\n    contradicted: freshness.contradicted,\n    archived: freshness.archived,\n    contentHash: hashPageBody(raw.body),\n    sourceHashes: resolveSourceHashes(sources, sourceHashes),\n    ...(typeof meta.modelId === \"string\" ? { modelId: meta.modelId } : {}),\n    ...(typeof meta.promptVersion === \"string\" ? { promptVersion: meta.promptVersion } : {}),\n  };\n}\n\n/**\n * Collect all exportable wiki pages from `wiki/concepts/` and `wiki/queries/`.\n * Drops untitled records, frontmatter-orphaned records, and computed-orphaned\n * records (every owning source deleted) — those are diagnosed by lint/the\n * viewer, not exported. The freshness snapshot is built once and shared across\n * all pages. Returns the surviving pages sorted by title.\n */\nexport async function collectExportPages(root: string): Promise<ExportPage[]> {\n  const raw = await collectRawWikiPages(root);\n  const snapshot = await buildFreshnessSnapshot(root);\n  const sourceHashes = sourceHashLookupFromSnapshot(snapshot);\n  const kept = raw.filter((page) => page.parseStatus.hasTitle && !page.parseStatus.orphaned);\n  const pages = kept\n    .map((page) => toExportPage(page, snapshot, sourceHashes))\n    .filter((page) => page.freshnessStatus !== \"orphaned\");\n  pages.sort((a, b) => a.title.localeCompare(b.title));\n  return pages;\n}\n","/**\n * Export provenance helpers (export provenance).\n *\n * Surfaces the auditable lineage a downstream consumer (e.g. a downstream rule importer)\n * needs to answer \"this page came from these sources, via this model and\n * prompt version\":\n *\n *  - {@link hashPageBody} derives a deterministic SHA-256 over a page body so\n *    a consumer can detect content drift without re-reading the markdown.\n *  - {@link sourceHashLookupFromSnapshot} reuses a freshness snapshot's\n *    recorded per-source SHA-256 hashes as a filename → hash map.\n *  - {@link resolveSourceHashes} maps a page's `sources` frontmatter list to\n *    those committed hashes, preserving order and de-duplicating.\n *\n * The hashes here are the SAME digests `hasher.ts` writes to state.json — we\n * surface them rather than recompute, so the export stays consistent with the\n * compiler's own change-detection view and stays deterministic (no filesystem\n * re-reads, no wall-clock, no map-iteration order dependence).\n */\n\nimport { createHash } from \"node:crypto\";\nimport type { FreshnessSnapshot } from \"../freshness/types.js\";\n\n/** Map of source filename → committed SHA-256 hash from state.json. */\nexport type SourceHashLookup = Record<string, string>;\n\n/**\n * Deterministic SHA-256 (hex) of a page body. Stable for identical input:\n * the same body string always yields the same digest regardless of when or\n * where the export runs.\n * @param body - Full markdown page body (without frontmatter).\n * @returns Hex-encoded SHA-256 digest.\n */\nexport function hashPageBody(body: string): string {\n  return createHash(\"sha256\").update(body, \"utf-8\").digest(\"hex\");\n}\n\n/**\n * Build a filename -> source-hash lookup from an existing freshness snapshot.\n * The snapshot already contains state.json's recorded hashes, so export callers\n * that compute freshness can reuse the same read-only state pass.\n */\nexport function sourceHashLookupFromSnapshot(snapshot: FreshnessSnapshot): SourceHashLookup {\n  const lookup: SourceHashLookup = {};\n  for (const [file, source] of Object.entries(snapshot.sources)) {\n    lookup[file] = source.recordedHash;\n  }\n  return lookup;\n}\n\n/**\n * Resolve the source-file SHA-256 hashes a page derived from.\n *\n * Maps each entry in the page's `sources` frontmatter list to its committed\n * hash. Sources without a recorded hash (e.g. seed pages with an empty\n * source list, or a source removed from state) contribute nothing. Order\n * follows the `sources` list and duplicates collapse, so the output is\n * deterministic for a given (sources, state) pair.\n *\n * @param sources - Source filenames cited by the page (frontmatter `sources`).\n * @param lookup - Filename → hash map from {@link sourceHashLookupFromSnapshot}.\n * @returns Ordered, de-duplicated list of source hashes.\n */\nexport function resolveSourceHashes(\n  sources: string[],\n  lookup: SourceHashLookup,\n): string[] {\n  const hashes: string[] = [];\n  const seen = new Set<string>();\n  for (const file of sources) {\n    const hash = lookup[file];\n    if (hash === undefined || seen.has(hash)) continue;\n    hashes.push(hash);\n    seen.add(hash);\n  }\n  return hashes;\n}\n","/**\n * Project ID validation for the JSON export contract.\n *\n * The regex `PROJECT_ID_PATTERN` is mirrored byte-for-byte in\n * `@atomicmemory/llmwiki`'s importer-side `project-id.ts`. When you\n * change either, change both.\n *\n * `projectId` participates in the deterministic external IDs\n * (`llmwiki/<projectId>/<pageDirectory>/<slug>`) used by downstream\n * importers and the Atomic Memory namespace scope. It is therefore a\n * **security boundary**, not just a dedup aid: two projects supplying\n * the same `projectId` collide and silently overwrite each other\n * through any upsert primitive.\n *\n * Three guards apply:\n *\n *   1. Strict regex at the boundary (export side here; import side\n *      mirrors).\n *   2. The Atomic Memory write scope must authorize the namespace\n *      (enforced server-side by the adapter; out of scope for the\n *      exporter).\n *   3. Collision detection on import when an existing record's\n *      `source` field differs (also import side).\n *\n * The regex below pins the on-wire format: lowercase letters, digits,\n * and hyphens; must begin with letter or digit; 1..63 characters. The\n * length cap matches DNS-label conventions and keeps external IDs\n * fitting comfortably inside Atomic Memory's metadata indexing limits.\n */\n\n/** Regex pinning the on-wire `projectId` format. Mirrored on the importer side. */\nexport const PROJECT_ID_PATTERN = /^[a-z0-9][a-z0-9-]{0,62}$/;\n\n/**\n * Validate a candidate `projectId`. Returns the input string when the\n * input is valid; throws `Error` with a clear, actionable message\n * otherwise. The thrown message names the rejected value verbatim so\n * shell users see what they typed.\n */\nexport function validateProjectId(candidate: unknown): string {\n  if (typeof candidate !== \"string\") {\n    throw new Error(`projectId must be a string; received ${typeof candidate}`);\n  }\n  if (candidate.length === 0) {\n    throw new Error(\"projectId must not be empty\");\n  }\n  if (!PROJECT_ID_PATTERN.test(candidate)) {\n    throw new Error(\n      `Invalid projectId \"${candidate}\". ` +\n        `Must match /^[a-z0-9][a-z0-9-]{0,62}$/ (lowercase letters, digits, hyphens; ` +\n        `starts with letter or digit; max 63 characters).`,\n    );\n  }\n  return candidate;\n}\n","/**\n * JSON export format writer.\n *\n * Produces a structured JSON document containing all wiki pages and their\n * metadata. The schema is intentionally simple and human-readable so it can\n * be consumed directly by scripts, agents, or downstream pipelines without\n * additional transformation.\n *\n * Schema:\n *   { schemaVersion, exportedAt, pageCount, projectId?, pages: ExportPage[] }\n *\n * W4 provenance lives PER PAGE (`ExportPage.modelId` / `promptVersion` plus\n * `contentHash` / `sourceHashes`), stamped into each page at compile time.\n * It is deliberately not summarized at the envelope level: a single\n * export-time model id would misattribute pages compiled under a different\n * model, which is exactly the lineage bug this avoids.\n *\n * `schemaVersion` lets downstream consumers (e.g. the rule importer) pin to a known\n * contract. Increment when a breaking field change lands; additive fields\n * do not require a bump.\n *\n * `projectId` is the optional bridge identifier. When present it pins the\n * on-disk export to a stable identity that downstream consumers (the\n * Atomic Memory adapter especially) use to derive deterministic external\n * IDs. Validation happens at the CLI/programmatic boundary, not here —\n * by the time we serialize, the value has been checked.\n */\n\nimport { validateProjectId } from \"./project-id.js\";\nimport type { ExportPage } from \"./types.js\";\n\n/**\n * Monotonically-incremented envelope version.\n * Bump when a breaking field change lands; additive additions do not require a bump.\n */\nexport const EXPORT_SCHEMA_VERSION = 1;\n\n/** Top-level shape of the JSON export file. */\nexport interface JsonExportDocument {\n  /**\n   * Contract version for downstream consumers. Start at 1; increment only on\n   * breaking envelope changes so consumers can pin a supported range.\n   */\n  schemaVersion: number;\n  exportedAt: string;\n  pageCount: number;\n  /** Optional bridge identifier. See `src/export/project-id.ts` for the validation rule. */\n  projectId?: string;\n  pages: ExportPage[];\n}\n\n/** Options accepted by {@link buildJsonExportDocument}. */\nexport interface BuildJsonExportOptions {\n  /**\n   * Optional project identifier. Validated against the bridge contract\n   * regex; throws if invalid so a malformed value never reaches disk.\n   */\n  projectId?: string;\n}\n\n/**\n * Build the JSON export document object from a list of export pages.\n * @param pages - Sorted array of export pages.\n * @param options - Optional bridge envelope fields (e.g. `projectId`).\n * @returns The structured JsonExportDocument object (not serialized).\n */\nexport function buildJsonExportDocument(\n  pages: ExportPage[],\n  options: BuildJsonExportOptions = {},\n): JsonExportDocument {\n  const doc: JsonExportDocument = {\n    schemaVersion: EXPORT_SCHEMA_VERSION,\n    exportedAt: new Date().toISOString(),\n    pageCount: pages.length,\n    pages,\n  };\n  if (options.projectId !== undefined) {\n    doc.projectId = validateProjectId(options.projectId);\n  }\n  return doc;\n}\n\n/**\n * Build the JSON export document from a list of export pages.\n * @param pages - Sorted array of export pages.\n * @param options - Optional bridge envelope fields (e.g. `projectId`).\n * @returns Pretty-printed JSON string.\n */\nexport function buildJsonExport(\n  pages: ExportPage[],\n  options: BuildJsonExportOptions = {},\n): string {\n  return JSON.stringify(buildJsonExportDocument(pages, options), null, 2);\n}\n","/**\n * GraphML export format writer.\n *\n * Produces a GraphML XML document representing the wiki link graph.\n * Each page becomes a node; each [[wikilink]] between pages becomes a\n * directed edge. Node attributes carry page metadata (title, summary, tags).\n *\n * GraphML is the standard XML format for graph exchange and is supported by\n * Gephi, yEd, NetworkX, and many other graph tools.\n */\n\nimport type { ExportPage } from \"./types.js\";\n\n/** XML special characters that must be escaped in attribute values and text. */\nconst XML_ESCAPES: Record<string, string> = {\n  \"&\": \"&amp;\",\n  \"<\": \"&lt;\",\n  \">\": \"&gt;\",\n  '\"': \"&quot;\",\n  \"'\": \"&apos;\",\n};\n\n/** Escape a string for safe inclusion in XML. */\nfunction escapeXml(value: string): string {\n  return value.replace(/[&<>\"']/g, (ch) => XML_ESCAPES[ch] ?? ch);\n}\n\n/** GraphML attribute key definitions. */\nconst KEY_DEFS = [\n  '<key id=\"title\"     for=\"node\" attr.name=\"title\"     attr.type=\"string\"/>',\n  '<key id=\"summary\"   for=\"node\" attr.name=\"summary\"   attr.type=\"string\"/>',\n  '<key id=\"tags\"      for=\"node\" attr.name=\"tags\"      attr.type=\"string\"/>',\n  '<key id=\"sources\"   for=\"node\" attr.name=\"sources\"   attr.type=\"string\"/>',\n  '<key id=\"createdAt\" for=\"node\" attr.name=\"createdAt\" attr.type=\"string\"/>',\n  '<key id=\"updatedAt\" for=\"node\" attr.name=\"updatedAt\" attr.type=\"string\"/>',\n].join(\"\\n  \");\n\n/** Serialise one ExportPage as a GraphML <node> element. */\nfunction pageToNode(page: ExportPage): string {\n  const tags = page.tags.join(\", \");\n  const sources = page.sources.join(\", \");\n  return [\n    `  <node id=\"${escapeXml(page.slug)}\">`,\n    `    <data key=\"title\">${escapeXml(page.title)}</data>`,\n    `    <data key=\"summary\">${escapeXml(page.summary)}</data>`,\n    `    <data key=\"tags\">${escapeXml(tags)}</data>`,\n    `    <data key=\"sources\">${escapeXml(sources)}</data>`,\n    `    <data key=\"createdAt\">${escapeXml(page.createdAt)}</data>`,\n    `    <data key=\"updatedAt\">${escapeXml(page.updatedAt)}</data>`,\n    `  </node>`,\n  ].join(\"\\n\");\n}\n\n/** Build all <edge> elements for a single source page's outgoing links. */\nfunction pageToEdges(page: ExportPage, knownSlugs: Set<string>): string[] {\n  return page.links\n    .filter((slug) => knownSlugs.has(slug))\n    .map(\n      (slug) =>\n        `  <edge source=\"${escapeXml(page.slug)}\" target=\"${escapeXml(slug)}\"/>`,\n    );\n}\n\n/**\n * Build the GraphML document from a list of export pages.\n * Only edges whose target slug exists in the page set are included so the\n * graph contains no dangling references.\n * @param pages - Sorted array of export pages.\n * @returns GraphML XML string.\n */\nexport function buildGraphml(pages: ExportPage[]): string {\n  const knownSlugs = new Set(pages.map((p) => p.slug));\n  const nodes = pages.map(pageToNode).join(\"\\n\");\n  const edges = pages.flatMap((p) => pageToEdges(p, knownSlugs)).join(\"\\n\");\n\n  return [\n    '<?xml version=\"1.0\" encoding=\"UTF-8\"?>',\n    '<graphml xmlns=\"http://graphml.graphdrawing.org/graphml\"',\n    '         xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"',\n    '         xsi:schemaLocation=\"http://graphml.graphdrawing.org/graphml',\n    '           http://graphml.graphdrawing.org/graphml/1.0/graphml.xsd\">',\n    `  ${KEY_DEFS}`,\n    '  <graph id=\"wiki\" edgedefault=\"directed\">',\n    nodes,\n    edges,\n    \"  </graph>\",\n    \"</graphml>\",\n    \"\",\n  ].join(\"\\n\");\n}\n","/**\n * Health score evaluator for the llmwiki eval harness.\n *\n * Aggregates the output of all 10+ lint rules into a single 0–100 score.\n * Errors on critical rules (broken links/citations, duplicates) cost 4 pts\n * each; contradicted pages cost 2 pts; all other warnings/info cost 1 pt each.\n * The final score is clamped to [0, 100].\n */\n\nimport {\n  checkBrokenWikilinks,\n  checkBrokenCitations,\n  checkMalformedClaimCitations,\n  checkOrphanedPages,\n  checkMissingSummaries,\n  checkDuplicateConcepts,\n  checkEmptyPages,\n  checkLowConfidencePages,\n  checkContradictedPages,\n  checkInferredWithoutCitations,\n  checkSchemaCrossLinks,\n} from \"../linter/rules.js\";\nimport { loadSchema } from \"../schema/loader.js\";\nimport type { LintResult } from \"../linter/types.js\";\nimport type { HealthResult, HealthRuleResult } from \"./types.js\";\n\nconst MAX_SCORE = 100;\nconst ERROR_DEDUCTION = 4;\nconst CONTRADICTED_DEDUCTION = 2;\nconst DEFAULT_DEDUCTION = 1;\n\n/** Rules treated as high-severity errors (−4 pts per violation). */\nconst ERROR_RULES = new Set([\n  \"broken-wikilink\",\n  \"broken-citation\",\n  \"duplicate-concept\",\n]);\n\n/** Compute the point deduction for a single lint result. */\nfunction deductionFor(result: LintResult): number {\n  if (ERROR_RULES.has(result.rule)) return ERROR_DEDUCTION;\n  if (result.rule === \"contradicted-page\") return CONTRADICTED_DEDUCTION;\n  return DEFAULT_DEDUCTION;\n}\n\n/** Aggregate lint results into a per-rule summary with deduction totals. */\nfunction aggregateRules(results: LintResult[]): HealthRuleResult[] {\n  const map = new Map<string, HealthRuleResult>();\n  for (const result of results) {\n    const existing = map.get(result.rule);\n    const deduction = deductionFor(result);\n    if (existing) {\n      existing.count++;\n      existing.deduction += deduction;\n    } else {\n      map.set(result.rule, {\n        rule: result.rule,\n        count: 1,\n        severity: result.severity,\n        deduction,\n      });\n    }\n  }\n  return Array.from(map.values());\n}\n\n/**\n * Run all lint rules against the project root and return an aggregated\n * health score plus per-rule breakdown.\n * @param root - Absolute path to the project root.\n */\nexport async function evaluateHealth(root: string): Promise<HealthResult> {\n  const schema = await loadSchema(root);\n\n  const allResults = (\n    await Promise.all([\n      checkBrokenWikilinks(root),\n      checkBrokenCitations(root),\n      checkMalformedClaimCitations(root),\n      checkOrphanedPages(root),\n      checkMissingSummaries(root),\n      checkDuplicateConcepts(root),\n      checkEmptyPages(root),\n      checkLowConfidencePages(root),\n      checkContradictedPages(root),\n      checkInferredWithoutCitations(root),\n      checkSchemaCrossLinks(root, schema),\n    ])\n  ).flat();\n\n  const rules = aggregateRules(allResults);\n  const totalDeduction = rules.reduce((sum, r) => sum + r.deduction, 0);\n  const score = Math.max(0, MAX_SCORE - totalDeduction);\n\n  return { score, maxScore: MAX_SCORE, rules };\n}\n","/**\n * Citation coverage evaluator for the llmwiki eval harness.\n *\n * Measures two things:\n *  - Coverage: what fraction of prose paragraphs contain at least one citation.\n *  - Precision: what fraction of citations point to a source file that exists.\n *\n * Non-prose paragraphs (headings, code blocks, lists, blank lines) are excluded\n * so that only human-readable claim text is counted.\n */\n\nimport path from \"path\";\nimport { collectAllPages } from \"../linter/rules.js\";\nimport { parseFrontmatter, extractClaimCitations, splitProseParagraphs } from \"../utils/markdown.js\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\nimport { resolveSourceFile } from \"./source-path.js\";\nimport type { CitationCoverageResult, CitationPageResult } from \"./types.js\";\n\n/** Prose paragraphs start with a Unicode letter. */\ninterface PageStats {\n  pageResult: CitationPageResult;\n  proseParagraphs: number;\n  citedParagraphs: number;\n  totalCitations: number;\n  validCitations: number;\n}\n\n/** Evaluate citation coverage and precision for a single page body. */\nasync function evaluatePage(slug: string, body: string, sourcesDir: string): Promise<PageStats> {\n  const paragraphs = splitProseParagraphs(body);\n  let citedParagraphs = 0;\n  let totalCitations = 0;\n  let validCitations = 0;\n\n  for (const para of paragraphs) {\n    const citations = extractClaimCitations(para);\n    if (citations.length === 0) continue;\n    citedParagraphs++;\n    for (const { spans } of citations) {\n      for (const span of spans) {\n        totalCitations++;\n        if ((await resolveSourceFile(sourcesDir, span.file)) !== null) validCitations++;\n      }\n    }\n  }\n\n  return {\n    pageResult: { slug, proseParagraphs: paragraphs.length, citedParagraphs },\n    proseParagraphs: paragraphs.length,\n    citedParagraphs,\n    totalCitations,\n    validCitations,\n  };\n}\n\n/**\n * Measure citation coverage and precision across all wiki pages.\n * @param root - Absolute path to the project root.\n */\nexport async function evaluateCitationCoverage(\n  root: string,\n): Promise<CitationCoverageResult> {\n  const pages = await collectAllPages(root);\n  const sourcesDir = path.join(root, SOURCES_DIR);\n\n  let totalProse = 0;\n  let totalCited = 0;\n  let totalCitations = 0;\n  let totalValid = 0;\n  const perPage: CitationPageResult[] = [];\n\n  for (const { filePath, content } of pages) {\n    const { body } = parseFrontmatter(content);\n    const slug = path.basename(filePath, \".md\");\n    const stats = await evaluatePage(slug, body, sourcesDir);\n    totalProse += stats.proseParagraphs;\n    totalCited += stats.citedParagraphs;\n    totalCitations += stats.totalCitations;\n    totalValid += stats.validCitations;\n    perPage.push(stats.pageResult);\n  }\n\n  const coveragePercent = totalProse === 0 ? 0 : (totalCited / totalProse) * 100;\n  const precisionPercent = totalCitations === 0 ? 0 : (totalValid / totalCitations) * 100;\n\n  return {\n    totalProseParagraphs: totalProse,\n    citedParagraphs: totalCited,\n    coveragePercent,\n    totalCitations,\n    validCitations: totalValid,\n    precisionPercent,\n    perPage,\n  };\n}\n","/**\n * Safe source-file resolver for the eval harness.\n *\n * Citation markers in wiki pages contain free-form file paths. Before the\n * eval harness reads any file or checks its existence, the path must be\n * confined to the project's `sources/` directory. Three independent layers\n * of defense are applied in order:\n *\n *   1. Structural: reject empty strings, absolute paths, and any `..` segment.\n *   2. Pre-realpath: resolve the joined path and verify it stays under sourcesDir.\n *   3. Symlink: call `fs.realpath` on both sides and verify again, catching\n *      symlinks inside sources/ that point outside the tree.\n *\n * The confinement pattern mirrors `resolveSafePath` in src/context/provenance.ts.\n */\n\nimport { realpath } from \"fs/promises\";\nimport path from \"path\";\n\n/**\n * True when any `/`- or `\\`-separated segment of `file` is literally `..`.\n * Splitting on both separators ensures a `nested\\..\\escape.md` path written\n * for a Windows consumer is also caught on Linux where `\\` is a valid filename\n * character.\n */\nfunction containsParentSegment(file: string): boolean {\n  return file.split(/[/\\\\]/).some((seg) => seg === \"..\");\n}\n\n/** True when `candidate` equals `parent` or sits beneath it. */\nfunction isInside(parent: string, candidate: string): boolean {\n  if (candidate === parent) return true;\n  const parentWithSep = parent.endsWith(path.sep) ? parent : parent + path.sep;\n  return candidate.startsWith(parentWithSep);\n}\n\n/**\n * Resolve `file` under `sourcesDir`, rejecting:\n *   - empty strings and absolute paths (`/etc/passwd`)\n *   - any path segment that is literally `..` (traversal, even normalizing back\n *     inside sources/ is rejected — the raw marker must be unambiguous)\n *   - paths that resolve outside `sourcesDir` after normalization\n *   - paths whose `realpath` escapes `sourcesDir` (symlink escapes)\n *\n * Returns the canonical absolute path on success, or `null` if the path is\n * rejected, the sources directory does not exist, or the file is not found.\n *\n * @param sourcesDir - Absolute path to the project's sources/ directory.\n * @param file - Relative file path from a citation marker (untrusted input).\n */\nexport async function resolveSourceFile(\n  sourcesDir: string,\n  file: string,\n): Promise<string | null> {\n  if (file.length === 0 || path.isAbsolute(file)) return null;\n  if (containsParentSegment(file)) return null;\n  const joined = path.join(sourcesDir, file);\n  if (!isInside(sourcesDir, path.resolve(joined))) return null;\n  try {\n    const realDir = await realpath(sourcesDir);\n    const realFile = await realpath(joined);\n    if (!isInside(realDir, realFile)) return null;\n    return realFile;\n  } catch {\n    return null;\n  }\n}\n","/**\n * Source utilization evaluator for the llmwiki eval harness.\n *\n * Measures whether every ingested source has been compiled into the wiki.\n * An uncited source means its concepts were either not extracted or not\n * linked to any generated page — a silent failure mode that no existing\n * lint rule catches.\n *\n * Algorithm: enumerate on-disk source files, resolve each through\n * resolveSourceFile to a canonical realpath, then cross-reference with\n * citation targets resolved the same way. Both sides use the same confined\n * resolver so symlinks and path differences are handled consistently.\n * When no valid sources remain after filtering, utilizationRate is null\n * (\"not measured\").\n */\n\nimport { readdir, lstat } from \"fs/promises\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport { collectAllPages } from \"../linter/rules.js\";\nimport { parseFrontmatter, extractClaimCitations, splitProseParagraphs } from \"../utils/markdown.js\";\nimport { resolveSourceFile } from \"./source-path.js\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\nimport type { SourceUtilizationResult } from \"./types.js\";\n\nfunction collectRawCitedFiles(body: string): Set<string> {\n  const files = new Set<string>();\n  for (const para of splitProseParagraphs(body)) {\n    const citations = extractClaimCitations(para);\n    for (const { spans } of citations) {\n      for (const span of spans) files.add(span.file);\n    }\n  }\n  return files;\n}\n\nasync function listSourceFiles(dir: string): Promise<string[]> {\n  if (!existsSync(dir)) return [];\n  const entries = await readdir(dir);\n  return entries.filter((e) => e.endsWith(\".md\"));\n}\n\nfunction pageSlug(filePath: string): string {\n  const dir = path.basename(path.dirname(filePath));\n  return dir + \"/\" + path.basename(filePath, \".md\");\n}\n\ninterface InventoryResult {\n  /** Names of source files that passed confinement (the valid inventory). */\n  validFiles: string[];\n  /** Map from valid source filename to its canonical realpath. */\n  fileToReal: Map<string, string>;\n  /** Non-fatal issues (e.g. out-of-tree symlinks excluded). */\n  warnings: string[];\n}\n\n/**\n * Build the filtered source inventory by resolving every on-disk source\n * through resolveSourceFile — the same confined resolver used for citation\n * targets. Files that fail resolution are excluded from the inventory and\n * reported as warnings. The caller MUST derive totalSources, perSource,\n * and cited/uncited counts from the returned validFiles, never from the\n * raw readdir() result.\n */\n/**\n * Explain why a source file was excluded from the inventory. The common case is\n * a symlink whose target is missing or resolves outside the sources tree;\n * everything else (bad path, unreadable) collapses to a generic reason.\n */\nasync function exclusionReason(sourcesDir: string, file: string): Promise<string> {\n  const stat = await lstat(path.join(sourcesDir, file)).catch(() => null);\n  return stat?.isSymbolicLink()\n    ? \"symlink target missing or outside sources/ (excluded)\"\n    : \"could not be resolved (excluded)\";\n}\n\nasync function resolveSourceInventory(\n  sourcesDir: string,\n  sourceFiles: string[],\n): Promise<InventoryResult> {\n  const fileToReal = new Map<string, string>();\n  const validFiles: string[] = [];\n  const warnings: string[] = [];\n  for (const f of sourceFiles) {\n    const resolved = await resolveSourceFile(sourcesDir, f);\n    if (resolved === null) {\n      // Filename first so the actionable detail survives any display\n      // truncation; distinguish the common symlink case from other failures.\n      warnings.push(`${f}: ${await exclusionReason(sourcesDir, f)}`);\n    } else {\n      fileToReal.set(f, resolved);\n      validFiles.push(f);\n    }\n  }\n  return { validFiles, fileToReal, warnings };\n}\n\nasync function collectCitedRealpaths(\n  sourcesDir: string,\n  pages: Array<{ filePath: string; content: string }>,\n): Promise<Map<string, Set<string>>> {\n  const citedRealToPages = new Map<string, Set<string>>();\n  for (const { filePath, content } of pages) {\n    const { body } = parseFrontmatter(content);\n    const slug = pageSlug(filePath);\n    for (const rawFile of collectRawCitedFiles(body)) {\n      const resolved = await resolveSourceFile(sourcesDir, rawFile);\n      if (resolved === null) continue;\n      const entry = citedRealToPages.get(resolved);\n      if (entry) entry.add(slug);\n      else citedRealToPages.set(resolved, new Set([slug]));\n    }\n  }\n  return citedRealToPages;\n}\n\nfunction buildPerSource(\n  validFiles: string[],\n  fileToReal: Map<string, string>,\n  citedRealToPages: Map<string, Set<string>>,\n): SourceUtilizationResult[\"perSource\"] {\n  const records = validFiles.map((sourceFile) => {\n    const real = fileToReal.get(sourceFile);\n    const pageSlugs = real ? citedRealToPages.get(real) : undefined;\n    return {\n      sourceFile,\n      citingPageCount: pageSlugs ? pageSlugs.size : 0,\n      citingPages: pageSlugs ? [...pageSlugs].sort() : ([] as string[]),\n    };\n  });\n  records.sort((a, b) => {\n    if (a.citingPageCount !== b.citingPageCount) return b.citingPageCount - a.citingPageCount;\n    return a.sourceFile.localeCompare(b.sourceFile);\n  });\n  return records;\n}\n\nexport async function evaluateSourceUtilization(\n  root: string,\n): Promise<SourceUtilizationResult> {\n  const sourcesDir = path.join(root, SOURCES_DIR);\n  const rawFiles = await listSourceFiles(sourcesDir);\n\n  // Build the filtered inventory — all downstream counts must use this,\n  // never rawFiles.length.\n  const { validFiles, fileToReal, warnings } = await resolveSourceInventory(sourcesDir, rawFiles);\n  const totalSources = validFiles.length;\n\n  if (totalSources === 0) {\n    // When raw readdir found files but the confined resolver filtered\n    // them all out, carry those warnings forward so the caller can see\n    // *why* the inventory is empty.\n    const rawWarnings = rawFiles.length > 0 && warnings.length > 0\n      ? warnings\n      : [];\n    return {\n      totalSources: 0, citedSources: 0, uncitedSources: 0,\n      utilizationRate: null, perSource: [], warnings: rawWarnings,\n    };\n  }\n\n  const pages = await collectAllPages(root);\n  const citedRealToPages = await collectCitedRealpaths(sourcesDir, pages);\n  const perSource = buildPerSource(validFiles, fileToReal, citedRealToPages);\n\n  const citedCount = perSource.filter((e) => e.citingPageCount > 0).length;\n  return {\n    totalSources,\n    citedSources: citedCount,\n    uncitedSources: totalSources - citedCount,\n    utilizationRate: Math.round((citedCount / totalSources) * 1000) / 1000,\n    perSource,\n    warnings,\n  };\n}\n","/**\n * Citation depth evaluator for the llmwiki eval harness.\n *\n * Measures how precise citations are. A bare ^[file.md] says \"this paragraph\n * came from somewhere in that source\" — useful but vague. A claim-level\n * citation ^[file.md:42-58] pins the exact lines, which is auditable.\n *\n * Metrics:\n *  - claimLevelRate: fraction of citations that include a line range.\n *  - avgCitationsPerParagraph: citation density across prose paragraphs.\n */\n\nimport { collectAllPages } from \"../linter/rules.js\";\nimport { parseFrontmatter, extractClaimCitations, splitProseParagraphs } from \"../utils/markdown.js\";\nimport type { CitationDepthResult } from \"./types.js\";\n\ninterface PageCounts { total: number; precise: number; proseParagraphs: number; }\n\nfunction countPageCitations(body: string): PageCounts {\n  const paragraphs = splitProseParagraphs(body);\n  let total = 0;\n  let precise = 0;\n  for (const para of paragraphs) {\n    const citations = extractClaimCitations(para);\n    for (const { spans } of citations) {\n      for (const span of spans) {\n        total++;\n        if (span.lines) precise++;\n      }\n    }\n  }\n  return { total, precise, proseParagraphs: paragraphs.length };\n}\n\nexport async function evaluateCitationDepth(\n  root: string,\n): Promise<CitationDepthResult> {\n  const pages = await collectAllPages(root);\n  let totalCitations = 0;\n  let citationsWithLineRange = 0;\n  let totalProseParagraphs = 0;\n  for (const { content } of pages) {\n    const { body } = parseFrontmatter(content);\n    const counts = countPageCitations(body);\n    totalCitations += counts.total;\n    citationsWithLineRange += counts.precise;\n    totalProseParagraphs += counts.proseParagraphs;\n  }\n  const claimLevelRate = totalCitations === 0 ? 0 : citationsWithLineRange / totalCitations;\n  const avgCitationsPerParagraph = totalProseParagraphs === 0 ? 0\n    : totalCitations / totalProseParagraphs;\n  return {\n    totalCitations,\n    preciseCitations: citationsWithLineRange,\n    vagueCitations: totalCitations - citationsWithLineRange,\n    claimLevelRate: Math.round(claimLevelRate * 1000) / 1000,\n    avgCitationsPerParagraph,\n  };\n}\n","/**\n * LLM citation judge for the llmwiki eval harness.\n *\n * For each cited prose paragraph in the wiki, extracts the (claim, source span)\n * pair and asks an LLM judge whether the source actually supports the claim.\n * Scoring: 0 = unsupported, 1 = partial, 2 = fully supported.\n *\n * Uses deterministic hash-based sampling so the same N citations are evaluated\n * on every run (reproducible). Results are cached in .llmwiki/eval/citation-cache.jsonl\n * so subsequent runs skip already-judged pairs.\n */\n\nimport { createHash } from \"crypto\";\nimport { readFile, appendFile, mkdir } from \"fs/promises\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport { collectAllPages } from \"../linter/rules.js\";\nimport { parseFrontmatter, extractClaimCitations, splitProseParagraphs } from \"../utils/markdown.js\";\nimport { callClaude } from \"../utils/llm.js\";\nimport { SOURCES_DIR, DEFAULT_PROVIDER, PROVIDER_MODELS } from \"../utils/constants.js\";\nimport { resolveSourceFile } from \"./source-path.js\";\nimport type { LLMTool } from \"../utils/provider.js\";\nimport type { CitationJudgement, CitationSupportResult } from \"./types.js\";\nimport type { SourceSpan } from \"../utils/types.js\";\n\nconst CACHE_DIR = path.join(\".llmwiki\", \"eval\");\nconst CACHE_FILE = path.join(CACHE_DIR, \"citation-cache.jsonl\");\n/** Internal pair combining a claim paragraph with its cited source span. */\ninterface CitationPair {\n  claimHash: string;\n  pageSlug: string;\n  claimText: string;\n  citedFile: string;\n  spanText: string;\n  lineStart: number;\n  lineEnd: number;\n}\n\nconst JUDGE_TOOL: LLMTool = {\n  name: \"judge_citation\",\n  description: \"Rate how well the source excerpt supports the claim.\",\n  input_schema: {\n    type: \"object\",\n    properties: {\n      score: {\n        type: \"integer\",\n        enum: [0, 1, 2],\n        description:\n          \"0=not supported or contradicted, 1=partially supported, 2=fully supported\",\n      },\n      reason: { type: \"string\", description: \"One sentence explaining the rating.\" },\n    },\n    required: [\"score\", \"reason\"],\n  },\n};\n\nconst JUDGE_SYSTEM =\n  \"You are an expert fact-checker. Given a claim from a wiki article and a source excerpt, rate whether the source supports the claim. Be strict: partial credit only if the source addresses the claim but is incomplete. Important: if the source excerpt consists entirely of YAML frontmatter (metadata fields such as title, date, author, or tags between --- delimiters), treat it as non-evidence for any substantive claim and score it 0, unless the claim is explicitly about that metadata field.\";\n\n// Content-addressable fingerprint of the judge prompt + tool schema.\n// Any edit to JUDGE_SYSTEM or JUDGE_TOOL produces a new hash, automatically\n// invalidating cached judgements without requiring a manual version bump.\nconst JUDGE_CONFIG_HASH = createHash(\"sha256\")\n  .update(JUDGE_SYSTEM + JSON.stringify(JUDGE_TOOL))\n  .digest(\"hex\")\n  .slice(0, 8);\n\n/** Compute a stable 16-char hex hash for a (claim, span) pair. */\nfunction hashPair(claimText: string, spanText: string): string {\n  return createHash(\"sha256\").update(claimText + spanText).digest(\"hex\").slice(0, 16);\n}\n\n/** Derive a full cache key from content hash + judge config fingerprint + model. */\nfunction makeCacheKey(contentHash: string, model: string): string {\n  return createHash(\"sha256\")\n    .update(contentHash + JUDGE_CONFIG_HASH + model)\n    .digest(\"hex\")\n    .slice(0, 16);\n}\n\n/** Extract the text of specific lines from a file (1-indexed, inclusive). */\nasync function readSourceLines(filePath: string, start: number, end: number): Promise<string> {\n  const content = await readFile(filePath, \"utf-8\");\n  return content\n    .split(\"\\n\")\n    .slice(start - 1, end)\n    .join(\"\\n\");\n}\n\n/** Strip `^[...]` markers from a paragraph to get the bare claim text. */\nfunction stripCitationMarkers(paragraph: string): string {\n  return paragraph.replace(/\\^\\[[^\\]]+\\]/g, \"\").trim();\n}\n\n/** Build a CitationPair from one span, or null if the source file is missing or has no line range. */\nasync function buildSpanPair(\n  slug: string,\n  claimText: string,\n  span: SourceSpan,\n  sourcesDir: string,\n): Promise<CitationPair | null> {\n  if (!span.lines) return null;\n  const sourceFile = await resolveSourceFile(sourcesDir, span.file);\n  if (sourceFile === null) return null;\n  const spanText = await readSourceLines(sourceFile, span.lines.start, span.lines.end);\n  return {\n    claimHash: hashPair(claimText, spanText),\n    pageSlug: slug,\n    claimText,\n    citedFile: span.file,\n    spanText,\n    lineStart: span.lines.start,\n    lineEnd: span.lines.end,\n  };\n}\n\n/** Extract citation pairs from a single cited paragraph. */\nasync function extractParagraphPairs(\n  slug: string,\n  para: string,\n  sourcesDir: string,\n): Promise<CitationPair[]> {\n  const citations = extractClaimCitations(para);\n  if (citations.length === 0) return [];\n  const claimText = stripCitationMarkers(para);\n  const spans = citations.flatMap((c) => c.spans);\n  const pairs = await Promise.all(spans.map((s) => buildSpanPair(slug, claimText, s, sourcesDir)));\n  return pairs.filter((p): p is CitationPair => p !== null);\n}\n\n/** Extract citation pairs from a single page body. */\nasync function extractPagePairs(\n  slug: string,\n  body: string,\n  sourcesDir: string,\n): Promise<CitationPair[]> {\n  const paragraphs = splitProseParagraphs(body);\n  const results = await Promise.all(paragraphs.map((p) => extractParagraphPairs(slug, p, sourcesDir)));\n  return results.flat();\n}\n\n/**\n * Extract all (claim, source span) pairs from the wiki.\n * Only pairs with valid line ranges pointing to existing source files are included.\n * @param root - Absolute path to the project root.\n */\nexport async function extractCitationPairs(root: string): Promise<CitationPair[]> {\n  const pages = await collectAllPages(root);\n  const sourcesDir = path.join(root, SOURCES_DIR);\n  const all: CitationPair[] = [];\n  for (const { filePath, content } of pages) {\n    const { body } = parseFrontmatter(content);\n    const slug = path.basename(filePath, \".md\");\n    const pairs = await extractPagePairs(slug, body, sourcesDir);\n    all.push(...pairs);\n  }\n  return all;\n}\n\n/**\n * Select a stable sample of N pairs that resists churn as the corpus grows.\n *\n * Previously-sampled hashes are retained first; only empty slots are filled\n * from new pairs (sorted by claimHash for determinism). This means adding new\n * citations to the corpus never displaces an already-evaluated pair, so score\n * movement in reports reflects quality change rather than sample turnover.\n *\n * @param pairs - All extracted citation pairs.\n * @param sampleSize - Maximum number of pairs to return.\n * @param previousHashes - Hashes selected in the prior run (from the saved report).\n */\nexport function selectDeterministicSample(\n  pairs: CitationPair[],\n  sampleSize: number,\n  previousHashes: string[] = [],\n): CitationPair[] {\n  const pairByHash = new Map(pairs.map((p) => [p.claimHash, p]));\n  const retained = previousHashes.flatMap((h) => {\n    const p = pairByHash.get(h);\n    return p ? [p] : [];\n  });\n  if (retained.length >= sampleSize) return retained.slice(0, sampleSize);\n  const retainedSet = new Set(previousHashes);\n  const newPairs = pairs\n    .filter((p) => !retainedSet.has(p.claimHash))\n    .sort((a, b) => a.claimHash.localeCompare(b.claimHash));\n  return [...retained, ...newPairs].slice(0, sampleSize);\n}\n\n/** Load previously cached judgements keyed by claimHash. */\nasync function loadCachedJudgements(root: string): Promise<Map<string, CitationJudgement>> {\n  const cachePath = path.join(root, CACHE_FILE);\n  if (!existsSync(cachePath)) return new Map();\n  const content = await readFile(cachePath, \"utf-8\");\n  const map = new Map<string, CitationJudgement>();\n  for (const line of content.trim().split(\"\\n\").filter(Boolean)) {\n    try {\n      const entry = JSON.parse(line) as CitationJudgement;\n      map.set(entry.claimHash, entry);\n    } catch {\n      // Skip malformed cache lines\n    }\n  }\n  return map;\n}\n\n/** Append a single judgement to the cache file. */\nasync function appendCachedJudgement(root: string, judgement: CitationJudgement): Promise<void> {\n  await mkdir(path.join(root, CACHE_DIR), { recursive: true });\n  await appendFile(path.join(root, CACHE_FILE), JSON.stringify(judgement) + \"\\n\");\n}\n\n/** Resolve the current model identifier for recording in judgements. */\nfunction resolveModel(): string {\n  const provider = process.env.LLMWIKI_PROVIDER ?? DEFAULT_PROVIDER;\n  return process.env.LLMWIKI_MODEL ?? PROVIDER_MODELS[provider] ?? provider;\n}\n\n/** Call the LLM judge for a single (claim, span) pair. */\nasync function callJudge(pair: CitationPair, cacheKey: string, model: string): Promise<CitationJudgement> {\n  const userMessage =\n    `Claim: ${pair.claimText}\\n\\nSource (${pair.citedFile}, lines ${pair.lineStart}–${pair.lineEnd}):\\n${pair.spanText}`;\n\n  const raw = await callClaude({\n    system: JUDGE_SYSTEM,\n    messages: [{ role: \"user\", content: userMessage }],\n    tools: [JUDGE_TOOL],\n    maxTokens: 256,\n  });\n\n  const parsed = JSON.parse(raw) as { score: 0 | 1 | 2; reason: string };\n  return {\n    claimHash: cacheKey,\n    pageSlug: pair.pageSlug,\n    citedFile: pair.citedFile,\n    lineStart: pair.lineStart,\n    lineEnd: pair.lineEnd,\n    claimText: pair.claimText,\n    spanText: pair.spanText,\n    score: parsed.score,\n    reason: parsed.reason,\n    model,\n    timestamp: new Date().toISOString(),\n  };\n}\n\n/** Aggregate raw judgement scores into summary statistics. */\nfunction aggregateJudgements(judgements: CitationJudgement[]): Pick<\n  CitationSupportResult,\n  \"meanScore\" | \"fullySupported\" | \"partiallySupported\" | \"unsupported\"\n> {\n  const fullySupported = judgements.filter((j) => j.score === 2).length;\n  const partiallySupported = judgements.filter((j) => j.score === 1).length;\n  const unsupported = judgements.filter((j) => j.score === 0).length;\n  const meanScore =\n    judgements.length === 0\n      ? 0\n      : judgements.reduce((sum, j) => sum + j.score, 0) / judgements.length;\n  return { meanScore, fullySupported, partiallySupported, unsupported };\n}\n\n/**\n * Judge each non-cached pair in the sample, returning all collected judgements\n * and an error count. Throws if every non-cached call fails (credentials missing,\n * provider down, etc.) — an empty result would be meaningless.\n */\nasync function judgeNewPairs(\n  sample: CitationPair[],\n  cache: Map<string, CitationJudgement>,\n  root: string,\n): Promise<{ judgements: CitationJudgement[]; judgeErrors: number }> {\n  const model = resolveModel();\n  const judgements: CitationJudgement[] = [];\n  let judgeErrors = 0;\n  let newPairsAttempted = 0;\n  let firstError: unknown;\n\n  for (const pair of sample) {\n    const cacheKey = makeCacheKey(pair.claimHash, model);\n    const cached = cache.get(cacheKey);\n    if (cached) {\n      judgements.push(cached);\n    } else {\n      newPairsAttempted++;\n      try {\n        const judgement = await callJudge(pair, cacheKey, model);\n        await appendCachedJudgement(root, judgement);\n        judgements.push(judgement);\n      } catch (err) {\n        judgeErrors++;\n        if (firstError === undefined) firstError = err;\n      }\n    }\n  }\n\n  if (newPairsAttempted > 0 && judgeErrors === newPairsAttempted) {\n    const msg = firstError instanceof Error ? firstError.message : String(firstError);\n    throw new Error(`Citation judge failed for all ${judgeErrors} sampled pair(s): ${msg}`);\n  }\n\n  return { judgements, judgeErrors };\n}\n\n/**\n * Run the citation support judge across a stable sample of wiki citations.\n * Returns null if no citable paragraphs exist.\n * @param root - Absolute path to the project root.\n * @param sampleSize - Number of citation pairs to judge per run.\n * @param previousHashes - Hashes sampled in the prior run; retained to prevent sample churn.\n */\nexport async function evaluateCitationSupport(\n  root: string,\n  sampleSize = 20,\n  previousHashes: string[] = [],\n): Promise<CitationSupportResult | null> {\n  const allPairs = await extractCitationPairs(root);\n  if (allPairs.length === 0) return null;\n\n  const sample = selectDeterministicSample(allPairs, sampleSize, previousHashes);\n  const cache = await loadCachedJudgements(root);\n  const { judgements, judgeErrors } = await judgeNewPairs(sample, cache, root);\n\n  return {\n    sampledCount: judgements.length,\n    sampledHashes: sample.map((p) => p.claimHash),\n    totalCitations: allPairs.length,\n    judgeErrors,\n    ...aggregateJudgements(judgements),\n    judgements,\n  };\n}\n","/**\n * Corpus size stats collector for the llmwiki eval harness.\n *\n * Snapshots source count, page count, total wiki character count, and\n * embedding counts. Each run appends one JSON line to .llmwiki/eval/history.jsonl\n * for trend analysis over time.\n */\n\nimport { readdir, appendFile, mkdir, readFile } from \"fs/promises\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport { collectAllPages } from \"../linter/rules.js\";\nimport { parseFrontmatter } from \"../utils/markdown.js\";\nimport { readEmbeddingStore } from \"../utils/embeddings.js\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\nimport type { StatsResult, EvalReport } from \"./types.js\";\n\nconst HISTORY_DIR = path.join(\".llmwiki\", \"eval\");\nconst HISTORY_FILE = path.join(HISTORY_DIR, \"history.jsonl\");\n\n/** Count the number of files in a directory (non-recursive, ignores missing dir). */\nasync function countFiles(dir: string): Promise<number> {\n  if (!existsSync(dir)) return 0;\n  const entries = await readdir(dir);\n  return entries.filter((e) => e.endsWith(\".md\")).length;\n}\n\n/**\n * Collect a corpus size snapshot for the current project state.\n * @param root - Absolute path to the project root.\n */\nexport async function collectStats(root: string): Promise<StatsResult> {\n  const [sourceCount, pages, embeddingStore] = await Promise.all([\n    countFiles(path.join(root, SOURCES_DIR)),\n    collectAllPages(root),\n    readEmbeddingStore(root),\n  ]);\n\n  let totalWikiChars = 0;\n  for (const { content } of pages) {\n    const { body } = parseFrontmatter(content);\n    totalWikiChars += body.length;\n  }\n\n  const pageCount = pages.length;\n  const avgPageLengthChars = pageCount === 0 ? 0 : Math.round(totalWikiChars / pageCount);\n  const embeddingCount = embeddingStore?.entries.length ?? 0;\n  const chunkEmbeddingCount = embeddingStore?.chunks?.length ?? 0;\n\n  return {\n    timestamp: new Date().toISOString(),\n    sourceCount,\n    pageCount,\n    totalWikiChars,\n    embeddingCount,\n    chunkEmbeddingCount,\n    avgPageLengthChars,\n  };\n}\n\n/**\n * Append the current eval report as a single JSON line to history.jsonl.\n * Creates the directory if it does not exist.\n * @param root - Absolute path to the project root.\n * @param report - The completed EvalReport to persist.\n */\nexport async function appendHistory(root: string, report: EvalReport): Promise<void> {\n  const historyDir = path.join(root, HISTORY_DIR);\n  await mkdir(historyDir, { recursive: true });\n  await appendFile(path.join(root, HISTORY_FILE), JSON.stringify(report) + \"\\n\");\n}\n\n/**\n * Load the last N eval reports from history.jsonl, oldest first.\n * Returns an empty array if no history file exists or the file is empty.\n * @param root - Absolute path to the project root.\n * @param n - Maximum number of reports to return (default 10).\n */\nexport async function loadHistory(root: string, n = 10): Promise<EvalReport[]> {\n  const historyPath = path.join(root, HISTORY_FILE);\n  if (!existsSync(historyPath)) return [];\n\n  const content = await readFile(historyPath, \"utf-8\");\n  const lines = content.trim().split(\"\\n\").filter(Boolean);\n  const reports: EvalReport[] = [];\n  for (const line of lines.slice(-n)) {\n    try {\n      reports.push(JSON.parse(line) as EvalReport);\n    } catch {\n      // Skip malformed lines\n    }\n  }\n  return reports;\n}\n\n/** Read the history file and return its non-empty lines, or null if it doesn't exist. */\nasync function readHistoryLines(root: string): Promise<string[] | null> {\n  const historyPath = path.join(root, HISTORY_FILE);\n  if (!existsSync(historyPath)) return null;\n  const content = await readFile(historyPath, \"utf-8\");\n  return content.trim().split(\"\\n\").filter(Boolean);\n}\n\n/**\n * Load the most recent eval report from history.jsonl, or null if none exists.\n * @param root - Absolute path to the project root.\n */\nexport async function loadPreviousReport(root: string): Promise<EvalReport | null> {\n  const lines = await readHistoryLines(root);\n  if (!lines || lines.length === 0) return null;\n  try {\n    return JSON.parse(lines[lines.length - 1]) as EvalReport;\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Load the most recent full-suite eval report from history.jsonl, skipping fast-suite\n * entries. This ensures citation-support sampledHashes are not lost when a fast run\n * occurs between two full runs.\n * @param root - Absolute path to the project root.\n */\nexport async function loadLastFullReport(root: string): Promise<EvalReport | null> {\n  const lines = await readHistoryLines(root);\n  if (!lines) return null;\n  for (let i = lines.length - 1; i >= 0; i--) {\n    try {\n      const report = JSON.parse(lines[i]) as EvalReport;\n      if (report.suite === \"full\") return report;\n    } catch {\n      // Skip malformed lines\n    }\n  }\n  return null;\n}\n","/**\n * Regression detection for the llmwiki eval harness.\n *\n * Computes signed metric deltas between the current eval report and the\n * previous one from history.jsonl. Positive = improvement, negative = regression.\n * Fields are omitted when either report lacks the data (e.g. citationSupportMean\n * is only present on full-suite runs).\n */\n\nimport type { EvalReport, EvalDelta } from \"./types.js\";\n\n/**\n * Compute the signed difference between current and previous eval metrics.\n * @param current - The just-completed report.\n * @param previous - The last report loaded from history.jsonl.\n */\nexport function computeDelta(current: EvalReport, previous: EvalReport): EvalDelta {\n  const delta: EvalDelta = {\n    healthScore: current.health.score - previous.health.score,\n    citationCoveragePercent:\n      current.citationCoverage.coveragePercent - previous.citationCoverage.coveragePercent,\n    citationPrecisionPercent:\n      current.citationCoverage.precisionPercent - previous.citationCoverage.precisionPercent,\n  };\n\n  if (current.citationSupport !== undefined && previous.citationSupport !== undefined) {\n    delta.citationSupportMean =\n      current.citationSupport.meanScore - previous.citationSupport.meanScore;\n  }\n\n  return delta;\n}\n","/**\n * CI threshold gating for the llmwiki eval harness.\n *\n * Reads an optional .llmwiki/eval/thresholds.yaml config and checks whether\n * the current report meets each configured threshold. Returns a list of\n * human-readable violation messages; an empty list means all thresholds pass.\n *\n * Supported threshold keys:\n *   health_score              — minimum health score (0–100)\n *   citation_coverage_percent — minimum citation coverage (0–100)\n *   citation_precision_percent — minimum citation precision (0–100)\n *   citation_support_mean     — minimum mean judge score (0.0–2.0)\n *   source_utilization_rate   — minimum fraction of sources cited (0.0–1.0)\n *   source_warnings_max       — maximum source-inventory warnings allowed (integer)\n *   claim_level_citation_rate — minimum fraction of citations with line ranges (0.0–1.0)\n */\n\nimport { readFile } from \"fs/promises\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport yaml from \"js-yaml\";\nimport type { EvalReport } from \"./types.js\";\n\nconst THRESHOLDS_FILE = path.join(\".llmwiki\", \"eval\", \"thresholds.yaml\");\n\ninterface ThresholdConfig {\n  health_score?: number;\n  citation_coverage_percent?: number;\n  citation_precision_percent?: number;\n  citation_support_mean?: number;\n  /** Maximum number of judge call failures allowed per run (0 = any error fails CI). */\n  citation_judge_error_max?: number;\n  /** Minimum fraction of sources cited by ≥1 wiki page (0.0–1.0). */\n  source_utilization_rate?: number;\n  /**\n   * Maximum source-inventory warnings allowed (e.g. out-of-tree symlinks or\n   * unresolvable files excluded from the count). Gates inventory health, which\n   * is distinct from utilization — an excluded source is an invalid entry, not\n   * an uncited one. 0 = any excluded source fails CI.\n   */\n  source_warnings_max?: number;\n  claim_level_citation_rate?: number;\n}\n\n/** Load the threshold config from disk, or return an empty config if absent. */\nasync function loadThresholds(root: string): Promise<ThresholdConfig> {\n  const configPath = path.join(root, THRESHOLDS_FILE);\n  if (!existsSync(configPath)) return {};\n  const raw = await readFile(configPath, \"utf-8\");\n  return (yaml.load(raw) as ThresholdConfig) ?? {};\n}\n\n/** Check the source-utilization and citation-depth thresholds. */\nfunction checkNewThresholds(\n  violations: string[],\n  config: ThresholdConfig,\n  report: EvalReport,\n): void {\n  const util = report.sourceUtilization;\n  if (\n    config.source_utilization_rate !== undefined &&\n    util.utilizationRate !== null &&\n    util.totalSources > 0 &&\n    util.utilizationRate < config.source_utilization_rate\n  ) {\n    violations.push(\n      `source_utilization_rate ${(util.utilizationRate * 100).toFixed(1)}% is below threshold ${(config.source_utilization_rate * 100).toFixed(1)}%`,\n    );\n  }\n\n  if (config.source_warnings_max !== undefined && util.warnings.length > config.source_warnings_max) {\n    violations.push(\n      `source_warnings ${util.warnings.length} exceeds max ${config.source_warnings_max}`,\n    );\n  }\n\n  if (\n    config.claim_level_citation_rate !== undefined &&\n    report.citationDepth.claimLevelRate < config.claim_level_citation_rate\n  ) {\n    violations.push(\n      `claim_level_citation_rate ${(report.citationDepth.claimLevelRate * 100).toFixed(1)}% is below threshold ${(config.claim_level_citation_rate * 100).toFixed(1)}%`,\n    );\n  }\n}\n\n/**\n * Check the report against configured thresholds.\n * @param report - The completed eval report.\n * @param root - Absolute path to the project root.\n * @returns List of violation messages (empty = all pass).\n */\nexport async function checkThresholds(\n  report: EvalReport,\n  root: string,\n): Promise<string[]> {\n  const config = await loadThresholds(root);\n  const violations: string[] = [];\n\n  if (config.health_score !== undefined && report.health.score < config.health_score) {\n    violations.push(\n      `health_score ${report.health.score} is below threshold ${config.health_score}`,\n    );\n  }\n\n  if (\n    config.citation_coverage_percent !== undefined &&\n    report.citationCoverage.coveragePercent < config.citation_coverage_percent\n  ) {\n    violations.push(\n      `citation_coverage_percent ${report.citationCoverage.coveragePercent.toFixed(1)}% is below threshold ${config.citation_coverage_percent}%`,\n    );\n  }\n\n  if (\n    config.citation_precision_percent !== undefined &&\n    report.citationCoverage.precisionPercent < config.citation_precision_percent\n  ) {\n    violations.push(\n      `citation_precision_percent ${report.citationCoverage.precisionPercent.toFixed(1)}% is below threshold ${config.citation_precision_percent}%`,\n    );\n  }\n\n  if (\n    config.citation_support_mean !== undefined &&\n    report.citationSupport !== undefined &&\n    report.citationSupport.meanScore < config.citation_support_mean\n  ) {\n    violations.push(\n      `citation_support_mean ${report.citationSupport.meanScore.toFixed(2)} is below threshold ${config.citation_support_mean}`,\n    );\n  }\n\n  if (\n    config.citation_judge_error_max !== undefined &&\n    report.citationSupport !== undefined &&\n    report.citationSupport.judgeErrors > config.citation_judge_error_max\n  ) {\n    violations.push(\n      `citation_judge_errors ${report.citationSupport.judgeErrors} exceeds max ${config.citation_judge_error_max}`,\n    );\n  }\n\n  checkNewThresholds(violations, config, report);\n\n  return violations;\n}\n","/**\n * Report assembly for the llmwiki eval harness.\n *\n * Combines evaluated components (health, citation coverage, stats, citation support)\n * into a final EvalReport with delta tracking and threshold validation.\n * Shared by the CLI eval command and the MCP run_eval tool.\n */\n\nimport { evaluateHealth } from \"./health.js\";\nimport { evaluateCitationCoverage } from \"./citation-coverage.js\";\nimport { evaluateSourceUtilization } from \"./source-utilization.js\";\nimport { evaluateCitationDepth } from \"./citation-depth.js\";\nimport { evaluateCitationSupport } from \"./citation-support.js\";\nimport { collectStats, appendHistory, loadPreviousReport, loadLastFullReport } from \"./stats.js\";\nimport { computeDelta } from \"./delta.js\";\nimport { checkThresholds } from \"./thresholds.js\";\nimport { ensureProviderAvailable } from \"../utils/provider-guard.js\";\nimport type { EvalReport, HealthResult, CitationCoverageResult, SourceUtilizationResult, CitationDepthResult, CitationSupportResult, StatsResult } from \"./types.js\";\n\nexport const DEFAULT_SAMPLE_SIZE = 20;\n\ninterface EvalComponents {\n  health: HealthResult;\n  citationCoverage: CitationCoverageResult;\n  sourceUtilization: SourceUtilizationResult;\n  citationDepth: CitationDepthResult;\n  stats: StatsResult;\n  previousReport: EvalReport | null;\n  citationSupport?: CitationSupportResult | null;\n}\n\nasync function buildReport(root: string, components: EvalComponents, suite: \"fast\" | \"full\"): Promise<EvalReport> {\n  const { health, citationCoverage, sourceUtilization, citationDepth, stats, previousReport, citationSupport } = components;\n  const partial = {\n    suite,\n    timestamp: new Date().toISOString(),\n    health,\n    citationCoverage,\n    sourceUtilization,\n    citationDepth,\n    stats,\n    ...(citationSupport ? { citationSupport } : {}),\n  };\n  const delta = previousReport ? computeDelta(partial as EvalReport, previousReport) : undefined;\n  const thresholdViolations = await checkThresholds(partial as EvalReport, root);\n  return { ...partial, ...(delta ? { delta } : {}), thresholdViolations };\n}\n\n/** Run the full eval pipeline, optionally append to history, and return the report. */\nexport async function runEval(root: string, suite: \"fast\" | \"full\", sampleSize: number, record = true): Promise<EvalReport> {\n  if (suite === \"full\") ensureProviderAvailable();\n  const [health, citationCoverage, sourceUtilization, citationDepth, stats, previousReport, previousFullReport] = await Promise.all([\n    evaluateHealth(root),\n    evaluateCitationCoverage(root),\n    evaluateSourceUtilization(root),\n    evaluateCitationDepth(root),\n    collectStats(root),\n    loadPreviousReport(root),\n    suite === \"full\" ? loadLastFullReport(root) : Promise.resolve(null),\n  ]);\n  const citationSupport = suite === \"full\"\n    ? await evaluateCitationSupport(root, sampleSize, previousFullReport?.citationSupport?.sampledHashes ?? [])\n    : undefined;\n  const report = await buildReport(root, { health, citationCoverage, sourceUtilization, citationDepth, stats, previousReport, citationSupport }, suite);\n  if (record) await appendHistory(root, report);\n  return report;\n}\n","/**\n * Read-only project-status collector shared by the MCP `wiki_status` tool and the in-process SDK.\n *\n * Derives stale/orphaned page classification from the freshness module so\n * agents get source-level accuracy rather than frontmatter-only orphans.\n * Uses `readStateClassified` throughout — never `readState` — so corrupt\n * state.json never produces a `.bak` side-effect.\n *\n * `pendingChanges` is derived directly from the freshness snapshot (which\n * already has per-source currentHash/recordedHash/exists) plus a cheap\n * directory listing — no second hash pass. `detectChanges` is NOT called.\n */\n\nimport path from \"path\";\nimport { readdir } from \"fs/promises\";\nimport { collectPageSummaries, scanWikiPages } from \"../compiler/indexgen.js\";\nimport { countCandidates } from \"../compiler/candidates.js\";\nimport { readStateClassified } from \"../utils/state.js\";\nimport { buildFreshnessSnapshot, computeFreshness } from \"../freshness/index.js\";\nimport { CONCEPTS_DIR, QUERIES_DIR, SOURCES_DIR } from \"../utils/constants.js\";\nimport type { FreshnessSnapshot } from \"../freshness/types.js\";\n\n/**\n * Maximum number of items returned in each agent-facing list (stalePages,\n * orphanedPages, pendingChanges). Bounds the MCP response size and agent\n * context consumption on large wikis. True totals are in the matching *Count fields.\n */\nexport const MAX_STATUS_LIST = 100;\n\n/** Shape returned by `collectStatus` and surfaced by the `wiki_status` tool. */\nexport interface WikiStatus {\n  pages: { concepts: number; queries: number; total: number };\n  sources: number;\n  lastCompiledAt: string | null;\n  /**\n   * Concept slugs whose source changed or partially disappeared since compile.\n   * Capped at MAX_STATUS_LIST (sorted ascending); see staleCount for the true total.\n   */\n  stalePages: string[];\n  /** True total of stale pages (may exceed stalePages.length when capped). */\n  staleCount: number;\n  /**\n   * Concept slugs whose every owning source was deleted, or frontmatter-flagged orphaned.\n   * Capped at MAX_STATUS_LIST (sorted ascending); see orphanedCount for the true total.\n   */\n  orphanedPages: string[];\n  /** True total of orphaned pages (may exceed orphanedPages.length when capped). */\n  orphanedCount: number;\n  /** Readability of .llmwiki/state.json — surfaced so corrupt state is never silent. */\n  stateStatus: \"ok\" | \"missing\" | \"corrupt\";\n  /** Number of compile candidates awaiting human review. */\n  pendingCandidates: number;\n  /**\n   * Source files with changes since last compile (new/changed/deleted).\n   * Capped at MAX_STATUS_LIST (sorted by file); see pendingChangesCount for the true total.\n   */\n  pendingChanges: Array<{ file: string; status: string }>;\n  /** True total of pending changes (may exceed pendingChanges.length when capped). */\n  pendingChangesCount: number;\n}\n\n/** Classify scanned concept pages into stale/orphaned arrays using the freshness snapshot. */\nfunction classifyConceptPages(\n  scanned: { slug: string; meta: Record<string, unknown> }[],\n  snapshot: FreshnessSnapshot,\n): { stalePages: string[]; orphanedPages: string[] } {\n  const stalePages: string[] = [];\n  const orphanedPages: string[] = [];\n  for (const { slug, meta } of scanned) {\n    const { freshnessStatus } = computeFreshness(\n      { slug, pageDirectory: \"concepts\", frontmatter: meta },\n      snapshot,\n    );\n    if (freshnessStatus === \"stale\") stalePages.push(slug);\n    else if (freshnessStatus === \"orphaned\") orphanedPages.push(slug);\n  }\n  return { stalePages, orphanedPages };\n}\n\n/** Derive the last compile time from state sources, or null if no sources. */\nfunction lastCompileTime(sources: Record<string, { compiledAt: string }>): string | null {\n  const times = Object.values(sources).map((s) => s.compiledAt);\n  return times.length > 0 ? times.sort().slice(-1)[0] : null;\n}\n\n/** List markdown filenames in sources/ without hashing — cheap directory scan. */\nasync function listSourceFilesOnDisk(root: string): Promise<string[]> {\n  try {\n    const entries = await readdir(path.join(root, SOURCES_DIR));\n    return entries.filter((f) => f.endsWith(\".md\"));\n  } catch {\n    return [];\n  }\n}\n\n/**\n * Derive pending source changes (new/changed/deleted) from the freshness snapshot — no extra hashing.\n * The snapshot already contains recordedHash, currentHash, and exists for each tracked source,\n * so we only need a cheap directory listing to discover untracked (new) files.\n */\nfunction pendingChangesFromSnapshot(\n  snapshot: FreshnessSnapshot,\n  sourceFilesOnDisk: string[],\n): Array<{ file: string; status: string }> {\n  const out: Array<{ file: string; status: string }> = [];\n  for (const [file, s] of Object.entries(snapshot.sources)) {\n    if (!s.exists) out.push({ file, status: \"deleted\" });\n    else if (s.currentHash !== s.recordedHash) out.push({ file, status: \"changed\" });\n  }\n  const recorded = new Set(Object.keys(snapshot.sources));\n  for (const file of sourceFilesOnDisk) {\n    if (!recorded.has(file)) out.push({ file, status: \"new\" });\n  }\n  return out;\n}\n\n/**\n * Sort a slug list ascending and cap it at MAX_STATUS_LIST.\n * Deterministic truncation ensures agents see the same subset on repeated calls.\n */\nfunction capSlugs(slugs: string[]): string[] {\n  return slugs.slice().sort().slice(0, MAX_STATUS_LIST);\n}\n\n/**\n * Sort a pending-change list by file name ascending and cap at MAX_STATUS_LIST.\n * Deterministic truncation matches capSlugs behaviour for consistency.\n */\nfunction capPendingChanges(\n  changes: Array<{ file: string; status: string }>,\n): Array<{ file: string; status: string }> {\n  return changes.slice().sort((a, b) => a.file.localeCompare(b.file)).slice(0, MAX_STATUS_LIST);\n}\n\n/** Build a read-only status snapshot used by the `wiki_status` MCP tool. */\nexport async function collectStatus(root: string): Promise<WikiStatus> {\n  const classified = await readStateClassified(root);\n  const snapshot = await buildFreshnessSnapshot(root, classified);\n\n  const [conceptSummaries, queries, scannedConcepts, pendingCandidates, sourceFilesOnDisk] = await Promise.all([\n    collectPageSummaries(path.join(root, CONCEPTS_DIR)),\n    collectPageSummaries(path.join(root, QUERIES_DIR)),\n    scanWikiPages(path.join(root, CONCEPTS_DIR)),\n    countCandidates(root),\n    listSourceFilesOnDisk(root),\n  ]);\n\n  const { stalePages, orphanedPages } = classifyConceptPages(scannedConcepts, snapshot);\n\n  // Suppress pendingChanges only on corrupt state: comparing against an empty snapshot\n  // on corrupt state would classify every source file as \"new\", which is false precision.\n  // On missing state the snapshot is legitimately empty, so every on-disk source is \"new\" — correct.\n  const pendingChanges = classified.status === \"corrupt\"\n    ? []\n    : pendingChangesFromSnapshot(snapshot, sourceFilesOnDisk);\n\n  return {\n    pages: { concepts: conceptSummaries.length, queries: queries.length, total: conceptSummaries.length + queries.length },\n    sources: Object.keys(classified.state.sources).length,\n    lastCompiledAt: lastCompileTime(classified.state.sources),\n    stalePages: capSlugs(stalePages),\n    staleCount: stalePages.length,\n    orphanedPages: capSlugs(orphanedPages),\n    orphanedCount: orphanedPages.length,\n    stateStatus: classified.status,\n    pendingCandidates,\n    pendingChanges: capPendingChanges(pendingChanges),\n    pendingChangesCount: pendingChanges.length,\n  };\n}\n","/**\n * Semantic and LLM-based page retrieval for llmwiki.\n *\n * Exports `pickSearchSlugs`, which resolves relevant page slugs for a\n * question by trying chunk-level retrieval first (highest precision), then\n * page-level embedding search, then LLM-driven selection over the wiki index.\n * Exports `loadPageRecords`, which hydrates a list of slugs into full\n * `PageRecord` objects, silently dropping missing or orphaned entries.\n *\n * This module is shared between the MCP tool layer and the in-process SDK.\n */\n\nimport path from \"path\";\nimport { findRelevantChunks, findRelevantPages } from \"../utils/embeddings.js\";\nimport { selectPages } from \"../commands/query.js\";\nimport { safeReadFile } from \"../utils/markdown.js\";\nimport { CHUNK_TOP_K, INDEX_FILE } from \"../utils/constants.js\";\nimport { readPageRecord, type PageRecord } from \"../pages/read.js\";\n\n/** Deduplicate slugs while preserving the first-seen ordering. */\nfunction dedupePreservingOrder(slugs: string[]): string[] {\n  const seen = new Set<string>();\n  const out: string[] = [];\n  for (const slug of slugs) {\n    if (seen.has(slug)) continue;\n    seen.add(slug);\n    out.push(slug);\n  }\n  return out;\n}\n\n/**\n * Resolve search candidates. Tries chunk-level retrieval first (highest\n * precision), then falls back to page-level embeddings, then to LLM-driven\n * selection over the wiki index.\n *\n * @param root - Absolute path to the wiki workspace root.\n * @param question - The query used to rank pages.\n * @returns Ordered list of relevant page slugs.\n */\nexport async function pickSearchSlugs(root: string, question: string): Promise<string[]> {\n  try {\n    const chunks = await findRelevantChunks(root, question, CHUNK_TOP_K);\n    if (chunks.length > 0) return dedupePreservingOrder(chunks.map((c) => c.chunk.slug));\n  } catch {\n    // Chunk store unavailable — fall through to page-level embeddings.\n  }\n\n  try {\n    const candidates = await findRelevantPages(root, question);\n    if (candidates.length > 0) return candidates.map((c) => c.slug);\n  } catch {\n    // Embeddings unavailable — fall through to index-based selection.\n  }\n\n  const indexContent = await safeReadFile(path.join(root, INDEX_FILE));\n  const { pages } = await selectPages(question, indexContent);\n  return pages;\n}\n\n/**\n * Load full content for a list of slugs, skipping missing/orphaned pages.\n *\n * @param root - Absolute path to the wiki workspace root.\n * @param slugs - List of page slugs to hydrate.\n * @returns Populated page records for all found, non-orphaned pages.\n */\nexport async function loadPageRecords(root: string, slugs: string[]): Promise<PageRecord[]> {\n  const records: PageRecord[] = [];\n  for (const slug of slugs) {\n    const page = await readPageRecord(root, slug);\n    if (page) records.push(page);\n  }\n  return records;\n}\n","/**\n * Page-reading utilities for llmwiki.\n *\n * Exposes `readPageRecord`, which locates a wiki page by slug across the\n * priority-ordered page directories (concepts first, then queries), parses\n * its frontmatter, and returns a structured `PageRecord`. Orphaned pages are\n * silently skipped to match the query pipeline's behaviour.\n *\n * This module is shared between the MCP tool layer and the in-process SDK so\n * both consumers work from identical read semantics.\n */\n\nimport path from \"path\";\nimport { safeReadFile, parseFrontmatter } from \"../utils/markdown.js\";\nimport { CONCEPTS_DIR, QUERIES_DIR } from \"../utils/constants.js\";\n\n/** Directories searched (in priority order) when resolving a page slug. */\nconst PAGE_DIRS = [CONCEPTS_DIR, QUERIES_DIR];\n\n/** Shape returned by readPageRecord and search_pages for each matching page. */\nexport interface PageRecord {\n  slug: string;\n  title: string;\n  summary: string;\n  body: string;\n}\n\n/**\n * Locate a page by slug across the priority-ordered page directories,\n * skipping orphaned entries to match the query pipeline's behaviour.\n *\n * @param root - Absolute path to the wiki workspace root.\n * @param slug - Page slug without the `.md` extension.\n * @returns The parsed page record, or `null` if not found or orphaned.\n */\nexport async function readPageRecord(root: string, slug: string): Promise<PageRecord | null> {\n  for (const dir of PAGE_DIRS) {\n    const content = await safeReadFile(path.join(root, dir, `${slug}.md`));\n    if (!content) continue;\n\n    const { meta, body } = parseFrontmatter(content);\n    if (meta.orphaned) continue;\n\n    return {\n      slug,\n      title: typeof meta.title === \"string\" ? meta.title : slug,\n      summary: typeof meta.summary === \"string\" ? meta.summary : \"\",\n      body: body.trim(),\n    };\n  }\n  return null;\n}\n","/**\n * Path-safe page access primitives for the llmwiki in-process SDK.\n *\n * Exposes two public functions:\n *   - `getPage(root, ref)` — fetch a single page by directory + slug; returns\n *     the full `Page` shape (body included) or null when the file is absent.\n *   - `listPages(root, options)` — scan both page directories, read each page's\n *     body so wikilinks can be extracted, apply archive/orphan filters, sort,\n *     and return a cursor-paged slice.\n *\n * Design notes:\n *   - `links` are derived from the Markdown **body** via `extractWikilinkSlugs`,\n *     NOT from frontmatter.\n *   - `archived` and `orphaned` are boolean **frontmatter** flags.\n *   - `scanWikiPages` returns `{ slug, meta }` only (no body), so `listPages`\n *     always re-reads each file to extract body links even when `includeBody`\n *     is false.\n *   - Path safety is enforced at `getPage` entry via `assertSafeSlug`; symlink\n *     confinement is handled at a lower level by `scanWikiPages`.\n */\n\nimport path from \"path\";\nimport { scanWikiPages } from \"../compiler/indexgen.js\";\nimport { safeReadFile, parseFrontmatter } from \"../utils/markdown.js\";\nimport { extractWikilinkSlugs } from \"../wiki/collect.js\";\nimport { assertSafeSlug } from \"../viewer/path-safety.js\";\nimport { CONCEPTS_DIR, QUERIES_DIR } from \"../utils/constants.js\";\nimport type { PageDirectory } from \"../export/types.js\";\n\nexport type { PageDirectory };\n\n/** A reference to a specific page by its directory and slug. */\nexport interface PageRef {\n  pageDirectory: PageDirectory;\n  slug: string;\n}\n\n/** A fully-resolved in-memory representation of a single wiki page. */\nexport interface Page {\n  slug: string;\n  pageDirectory: PageDirectory;\n  title: string;\n  summary: string;\n  tags: string[];\n  /** Slugs of pages linked via `[[wikilinks]]` in the body. */\n  links: string[];\n  createdAt?: string;\n  updatedAt?: string;\n  /** True when frontmatter contains `orphaned: true`. */\n  orphaned: boolean;\n  /** True when frontmatter contains `archived: true`. */\n  archived: boolean;\n  /** Full markdown body, present only when `includeBody` is true or via `getPage`. */\n  body?: string;\n}\n\n/** Options for filtering and paginating `listPages`. */\nexport interface ListPagesOptions {\n  cursor?: string;\n  limit?: number;\n  includeBody?: boolean;\n  includeArchived?: boolean;\n  includeOrphaned?: boolean;\n}\n\n/** Result returned by `listPages`. */\nexport interface ListPagesResult {\n  pages: Page[];\n  /** Opaque cursor for the next page; absent when the listing is exhausted. */\n  cursor?: string;\n}\n\n/** Maps each PageDirectory to its project-relative path. */\nconst DIR_NAMES: Record<PageDirectory, string> = {\n  concepts: CONCEPTS_DIR,\n  queries: QUERIES_DIR,\n};\n\n/** All page directories in listing order. */\nconst PAGE_DIRECTORIES: PageDirectory[] = [\"concepts\", \"queries\"];\n\n/**\n * Build a Page from its directory, slug, parsed frontmatter, and body text.\n * Links are always extracted from the body so they reflect real wikilinks,\n * not any frontmatter list.\n */\nfunction buildPage(\n  dir: PageDirectory,\n  slug: string,\n  meta: Record<string, unknown>,\n  body: string,\n  includeBody: boolean,\n): Page {\n  return {\n    slug,\n    pageDirectory: dir,\n    title: typeof meta.title === \"string\" ? meta.title : slug,\n    summary: typeof meta.summary === \"string\" ? meta.summary : \"\",\n    tags: Array.isArray(meta.tags) ? meta.tags.map(String) : [],\n    links: extractWikilinkSlugs(body),\n    createdAt: typeof meta.createdAt === \"string\" ? meta.createdAt : undefined,\n    updatedAt: typeof meta.updatedAt === \"string\" ? meta.updatedAt : undefined,\n    orphaned: meta.orphaned === true,\n    archived: meta.archived === true,\n    ...(includeBody ? { body } : {}),\n  };\n}\n\n/**\n * Fetch a single page by directory and slug.\n *\n * Throws `PathSafetyError` for unsafe slug values. Returns `null` when the\n * page does not exist on disk.\n *\n * @param root - Absolute path to the wiki workspace root.\n * @param ref - Which directory and slug to load.\n */\nexport async function getPage(root: string, ref: PageRef): Promise<Page | null> {\n  assertSafeSlug(ref.slug);\n  const filePath = path.join(root, DIR_NAMES[ref.pageDirectory], `${ref.slug}.md`);\n  const content = await safeReadFile(filePath);\n  if (!content) return null;\n  const { meta, body } = parseFrontmatter(content);\n  return buildPage(ref.pageDirectory, ref.slug, meta, body, true);\n}\n\n/**\n * List pages from both wiki directories with optional filtering and cursor\n * pagination.\n *\n * Pages are sorted by `(pageDirectory, slug)` before slicing. Bodies are\n * omitted by default; pass `includeBody: true` to include them. 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