llm-wiki-compiler 0.2.0 → 0.3.0

package/dist/cli.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../src/cli.ts","../src/commands/ingest.ts","../src/utils/markdown.ts","../src/utils/constants.ts","../src/utils/output.ts","../src/ingest/web.ts","../src/ingest/file.ts","../src/commands/compile.ts","../src/compiler/index.ts","../src/utils/state.ts","../src/providers/anthropic.ts","../src/providers/openai.ts","../src/providers/ollama.ts","../src/providers/minimax.ts","../src/utils/claude-settings.ts","../src/utils/provider.ts","../src/utils/llm.ts","../src/utils/lock.ts","../src/compiler/prompts.ts","../src/compiler/hasher.ts","../src/compiler/deps.ts","../src/compiler/orphan.ts","../src/compiler/resolver.ts","../src/compiler/indexgen.ts","../src/compiler/obsidian.ts","../src/utils/embeddings.ts","../src/commands/query.ts","../src/commands/watch.ts","../src/linter/rules.ts","../src/linter/index.ts","../src/commands/lint.ts","../src/mcp/server.ts","../src/mcp/tools.ts","../src/mcp/provider-check.ts","../src/mcp/resources.ts"],"sourcesContent":["/**\n * CLI entry point for llmwiki — the knowledge compiler.\n *\n * Registers all commands (ingest, compile, query, watch, lint) via Commander.\n * Validates the correct API key for the selected LLM provider.\n * Designed for `npx llmwiki` or global install via `npm install -g llm-wiki-compiler`.\n */\n\nimport \"dotenv/config\";\nimport { createRequire } from \"module\";\nimport { Command } from \"commander\";\nimport ingestCommand from \"./commands/ingest.js\";\nimport compileCommand from \"./commands/compile.js\";\nimport queryCommand from \"./commands/query.js\";\nimport watchCommand from \"./commands/watch.js\";\nimport lintCommand from \"./commands/lint.js\";\nimport { startMCPServer } from \"./mcp/server.js\";\nimport { DEFAULT_PROVIDER } from \"./utils/constants.js\";\nimport { resolveAnthropicAuthFromEnv } from \"./utils/claude-settings.js\";\n\nconst require = createRequire(import.meta.url);\nconst { version } = require(\"../package.json\") as { version: string };\n\nconst program = new Command();\n\nprogram\n  .name(\"llmwiki\")\n  .description(\"The knowledge compiler — raw sources in, interlinked wiki out\")\n  .version(version);\n\nprogram\n  .command(\"ingest <source>\")\n  .description(\"Ingest a URL or local file into sources/\")\n  .action(async (source: string) => {\n    try {\n      await ingestCommand(source);\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"compile\")\n  .description(\"Compile sources/ into an interlinked wiki\")\n  .action(async () => {\n    try {\n      requireProvider();\n      await compileCommand();\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"query <question>\")\n  .description(\"Ask a question against the wiki\")\n  .option(\"--save\", \"Save the answer as a wiki page\")\n  .action(async (question: string, options: { save?: boolean }) => {\n    try {\n      requireProvider();\n      await queryCommand(process.cwd(), question, options);\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"watch\")\n  .description(\"Watch sources/ and auto-recompile on changes\")\n  .action(async () => {\n    try {\n      requireProvider();\n      await watchCommand();\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"lint\")\n  .description(\"Run rule-based quality checks against the wiki\")\n  .action(async () => {\n    try {\n      await lintCommand();\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"serve\")\n  .description(\"Start an MCP server exposing wiki tools and resources over stdio\")\n  .option(\"--root <dir>\", \"Project root directory\", process.cwd())\n  .action(async (options: { root: string }) => {\n    try {\n      // Per-tool credential checks happen inside the MCP layer so read-only\n      // tools and ingest still work without an API key.\n      await startMCPServer({ root: options.root, version });\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\n/** API key env var required per provider. Null means no key needed. */\nconst PROVIDER_KEY_VARS: Record<string, string | null> = {\n  anthropic: \"ANTHROPIC_API_KEY\",\n  openai: \"OPENAI_API_KEY\",\n  ollama: null,\n  minimax: \"MINIMAX_API_KEY\",\n};\n\n/** Exit with a helpful message if the selected provider's API key is missing. */\nfunction requireProvider(): void {\n  const provider = process.env.LLMWIKI_PROVIDER ?? DEFAULT_PROVIDER;\n\n  if (provider === \"anthropic\") {\n    const auth = resolveAnthropicAuthFromEnv();\n    if (!auth.apiKey && !auth.authToken) {\n      console.error(\n        `\\x1b[31mError:\\x1b[0m Anthropic credentials are required for the \"anthropic\" provider.\\n` +\n          `  Set one of: export ANTHROPIC_API_KEY=<your-key> OR export ANTHROPIC_AUTH_TOKEN=<your-token>`,\n      );\n      process.exit(1);\n    }\n    return;\n  }\n\n  const keyVar = PROVIDER_KEY_VARS[provider];\n\n  if (keyVar === undefined) {\n    console.error(\n      `\\x1b[31mError:\\x1b[0m Unknown provider \"${provider}\".\\n` +\n        `  Supported: ${Object.keys(PROVIDER_KEY_VARS).join(\", \")}`,\n    );\n    process.exit(1);\n  }\n\n  if (keyVar && !process.env[keyVar]) {\n    console.error(\n      `\\x1b[31mError:\\x1b[0m ${keyVar} environment variable is required for the \"${provider}\" provider.\\n` +\n        `  Set it with: export ${keyVar}=<your-key>`,\n    );\n    process.exit(1);\n  }\n}\n\nprogram.parse();\n","/**\n * Commander action for `llmwiki ingest <source>`.\n * Detects whether the source is a URL or local file, delegates to the\n * appropriate ingestion module, and saves the result as a markdown file\n * with YAML frontmatter in the sources/ directory.\n */\n\nimport path from \"path\";\nimport { mkdir, writeFile } from \"fs/promises\";\nimport { slugify, buildFrontmatter } from \"../utils/markdown.js\";\nimport { MAX_SOURCE_CHARS, MIN_SOURCE_CHARS, SOURCES_DIR } from \"../utils/constants.js\";\nimport * as output from \"../utils/output.js\";\nimport ingestWeb from \"../ingest/web.js\";\nimport ingestFile from \"../ingest/file.js\";\nimport type { IngestResult } 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/** 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 ${MIN_SOURCE_CHARS}).`\n      )\n    );\n  }\n}\n\n/** Build the full markdown document with frontmatter. */\nexport function buildDocument(\n  title: string,\n  source: string,\n  result: TruncateResult,\n): string {\n  const meta: Record<string, unknown> = {\n    title,\n    source,\n    ingestedAt: new Date().toISOString(),\n  };\n  if (result.truncated) {\n    meta.truncated = true;\n    meta.originalChars = result.originalChars;\n  }\n  const frontmatter = buildFrontmatter(meta);\n\n  return `${frontmatter}\\n\\n${result.content}\\n`;\n}\n\n/** Write the ingested document to the sources/ directory. */\nasync function saveSource(title: string, document: string): Promise<string> {\n  const filename = `${slugify(title)}.md`;\n  const destPath = path.join(SOURCES_DIR, filename);\n\n  await mkdir(SOURCES_DIR, { recursive: true });\n  await writeFile(destPath, document, \"utf-8\");\n\n  return destPath;\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) or a local file path (.md or .txt).\n * @returns Saved filename, character count, truncation flag, and source URI.\n */\nexport async function ingestSource(source: string): Promise<IngestResult> {\n  output.status(\"*\", output.info(`Ingesting: ${source}`));\n\n  const { title, content } = isUrl(source)\n    ? await ingestWeb(source)\n    : await ingestFile(source);\n\n  const result = enforceCharLimit(content);\n  enforceMinContent(result.content);\n  const document = buildDocument(title, source, result);\n  const savedPath = await saveSource(title, document);\n\n  return {\n    filename: path.basename(savedPath),\n    charCount: result.content.length,\n    truncated: result.truncated,\n    source,\n  };\n}\n\n/**\n * Ingest a source (URL or local file) and save it to the sources/ directory.\n * @param source - A URL (http/https) or a local file path (.md or .txt).\n */\nexport default async function ingest(source: string): Promise<void> {\n  const result = await ingestSource(source);\n  const savedPath = path.join(SOURCES_DIR, result.filename);\n\n  output.status(\n    \"+\",\n    output.success(`Saved ${output.bold(result.filename)} → ${output.source(savedPath)}`)\n  );\n  output.status(\"→\", output.dim(\"Next: llmwiki compile\"));\n}\n","/**\n * Markdown parsing and manipulation helpers.\n * Handles YAML frontmatter extraction, slugification, and atomic file writes\n * for wiki pages.\n */\n\nimport { writeFile, rename, readFile, mkdir } from \"fs/promises\";\nimport path from \"path\";\nimport yaml from \"js-yaml\";\n\n/** Convert a human-readable concept title to a filename slug. */\nexport function slugify(title: string): string {\n  return title\n    .toLowerCase()\n    .replace(/['']/g, \"\")\n    .replace(/[^\\w\\s-]/g, \"\")\n    .replace(/\\s+/g, \"-\")\n    .replace(/-+/g, \"-\")\n    .replace(/^-|-$/g, \"\");\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${dumped}\\n---`;\n}\n\n/** Parse YAML frontmatter from a markdown string. Returns { meta, body }. */\nexport function parseFrontmatter(content: string): {\n  meta: Record<string, unknown>;\n  body: string;\n} {\n  const match = content.match(/^---\\n([\\s\\S]*?)\\n---\\n?([\\s\\S]*)$/);\n  if (!match) {\n    return { meta: {}, body: content };\n  }\n\n  let meta: Record<string, unknown> = {};\n  try {\n    const parsed = yaml.load(match[1]);\n    if (parsed && typeof parsed === \"object\") {\n      meta = parsed as Record<string, unknown>;\n    }\n  } catch {\n    // Malformed YAML — return empty meta so callers degrade gracefully.\n  }\n  return { meta, body: match[2] };\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 single citations (^[source.md]) and multi-source (^[a.md, b.md]).\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 citationPattern = /\\^\\[([^\\]]+)\\]/g;\n  const filenames = new Set<string>();\n\n  let match;\n  while ((match = citationPattern.exec(body)) !== null) {\n    const inner = match[1];\n    for (const part of inner.split(\",\")) {\n      const trimmed = part.trim();\n      if (trimmed.length > 0) {\n        filenames.add(trimmed);\n      }\n    }\n  }\n\n  return [...filenames];\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/**\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 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/** 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-4-20250514\",\n  openai: \"gpt-4o\",\n  ollama: \"llama3.1\",\n  minimax: \"MiniMax-M2.7\",\n};\n\n/** Default Ollama API base URL. */\nexport const OLLAMA_DEFAULT_HOST = \"http://localhost:11434/v1\";\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\";\nexport const EMBEDDINGS_FILE = \".llmwiki/embeddings.json\";\n\n/** Number of most similar pages to return from embedding-based pre-filter. */\nexport const EMBEDDING_TOP_K = 15;\n\n/** Embedding model to use per provider. */\nexport const EMBEDDING_MODELS: Record<string, string> = {\n  anthropic: \"voyage-3-lite\",\n  openai: \"text-embedding-3-small\",\n  ollama: \"nomic-embed-text\",\n};\n","/**\n * ANSI colored terminal output helpers.\n * Provides consistent styling for compilation progress, status messages,\n * and streaming token display.\n */\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}${RESET}`;\n}\n\n/** Print a status line with an icon. */\nexport function status(icon: string, message: string): void {\n  console.log(`${icon} ${message}`);\n}\n\n/** Print a section header. */\nexport function header(title: string): void {\n  console.log(`\\n${BOLD}${title}${RESET}`);\n  console.log(dim(\"─\".repeat(Math.min(title.length + 4, 60))));\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 ${url}`);\n  }\n\n  return {\n    title: article.title || \"Untitled\",\n    htmlContent: article.content,\n  };\n}\n\n/** Convert HTML to clean markdown using Turndown. */\nfunction convertToMarkdown(html: string): string {\n  const turndown = new TurndownService({ headingStyle: \"atx\" });\n  return turndown.turndown(html);\n}\n\n/**\n * Ingest a web URL and return its content as markdown.\n * @param url - The URL to fetch and convert.\n * @returns An object with the extracted title and markdown content.\n * @throws On network failure or unparseable content.\n */\nexport default async function ingestWeb(url: string): Promise<WebIngestResult> {\n  const response = await fetchAndParse(url);\n  const html = await response.text();\n  const { title, htmlContent } = extractReadableContent(html, url);\n  const content = convertToMarkdown(htmlContent);\n\n  return { title, content };\n}\n","/**\n * Local file ingestion module.\n * Reads .md and .txt files from the local filesystem and returns their\n * content as markdown. Markdown files are returned as-is; plain text files\n * are wrapped in a markdown code block. All other extensions are rejected.\n */\n\nimport { readFile } from \"fs/promises\";\nimport path from \"path\";\n\nconst SUPPORTED_EXTENSIONS = new Set([\".md\", \".txt\"]);\n\ninterface FileIngestResult {\n  title: string;\n  content: string;\n}\n\n/** Derive a human-readable title from a filename (without extension). */\nfunction titleFromFilename(filePath: string): string {\n  const basename = path.basename(filePath, path.extname(filePath));\n  return basename.replace(/[-_]+/g, \" \").trim();\n}\n\n/** Wrap plain text content in a markdown fenced block. */\nfunction wrapPlainText(text: string): string {\n  return `\\`\\`\\`\\n${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<FileIngestResult> {\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 * Commander action for `llmwiki compile`.\n * Checks that sources exist, then delegates to the compilation orchestrator\n * to process all new and changed source files into wiki pages.\n */\n\nimport { existsSync } from \"fs\";\nimport { compile } from \"../compiler/index.js\";\nimport * as output from \"../utils/output.js\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\n\n/**\n * Run the compile command from the current working directory.\n * Exits early if no sources directory exists yet.\n */\nexport default async function compileCommand(): Promise<void> {\n  if (!existsSync(SOURCES_DIR)) {\n    output.status(\n      \"!\",\n      output.warn('No sources found. Run `llmwiki ingest <url>` first.'),\n    );\n    return;\n  }\n\n  await compile(process.cwd());\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  atomicWrite,\n  safeReadFile,\n  validateWikiPage,\n  slugify,\n  buildFrontmatter,\n  parseFrontmatter,\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  buildPagePrompt,\n  parseConcepts,\n} from \"./prompts.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 { addObsidianMeta, generateMOC } from \"./obsidian.js\";\nimport { updateEmbeddings } from \"../utils/embeddings.js\";\nimport * as output from \"../utils/output.js\";\nimport {\n  COMPILE_CONCURRENCY,\n  CONCEPTS_DIR,\n  INDEX_FILE,\n  SOURCES_DIR,\n} from \"../utils/constants.js\";\nimport pLimit from \"p-limit\";\nimport type {\n  CompileResult,\n  ExtractedConcept,\n  SourceChange,\n  SourceState,\n  WikiState,\n} from \"../utils/types.js\";\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 */\nexport async function compile(root: string): Promise<void> {\n  await compileAndReport(root);\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 * @returns Structured result describing what was compiled.\n */\nexport async function compileAndReport(root: string): 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);\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}\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): Promise<PageGenerationResult> {\n  const merged = mergeExtractions(extractions, frozenSlugs);\n  const limit = pLimit(COMPILE_CONCURRENCY);\n  const errors: string[] = [];\n  const pages = await Promise.all(\n    merged.map((entry) => limit(async () => {\n      const writeError = await generateMergedPage(root, entry);\n      if (writeError) errors.push(writeError);\n      return entry;\n    })),\n  );\n  return { pages, errors };\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/** Build the structured CompileResult and emit the CLI completion banner. */\nfunction summarizeCompile(\n  buckets: ChangeBuckets,\n  generation: PageGenerationResult,\n  extractions: ExtractionResult[],\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 (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 ${result.sourceFile}`);\n    }\n  }\n\n  return {\n    compiled: buckets.toCompile.length,\n    skipped: buckets.unchanged.length,\n    deleted: buckets.deleted.length,\n    concepts: generation.pages.map((entry) => entry.concept.concept),\n    pages: generation.pages.map((entry) => entry.slug),\n    errors,\n  };\n}\n\n/** Inner pipeline, runs under lock protection. Returns structured CompileResult. */\nasync function runCompilePipeline(root: string): Promise<CompileResult> {\n  const state = await readState(root);\n  const changes = await detectChanges(root, state);\n  augmentWithAffectedSources(changes, findAffectedSources(state, changes));\n\n  const buckets = bucketChanges(changes);\n  if (buckets.toCompile.length === 0 && buckets.deleted.length === 0) {\n    output.status(\"✓\", output.success(\"Nothing to compile — all sources up to date.\"));\n    return { ...emptyCompileResult(), skipped: buckets.unchanged.length };\n  }\n\n  printChangesSummary(changes);\n  await markDeletedAsOrphaned(root, buckets.deleted, state);\n\n  const frozenSlugs = findFrozenSlugs(state, changes);\n  reportFrozenSlugs(frozenSlugs);\n\n  const extractions = await runExtractionPhases(root, buckets.toCompile, state, changes);\n  await freezeFailedExtractions(root, extractions, frozenSlugs);\n\n  const generation = await generatePagesPhase(root, extractions, frozenSlugs);\n  await persistExtractionStates(root, extractions);\n\n  if (frozenSlugs.size > 0) {\n    await orphanUnownedFrozenPages(root, frozenSlugs);\n  }\n  await persistFrozenSlugs(root, frozenSlugs, extractions);\n\n  await finalizeWiki(root, generation.pages);\n  return summarizeCompile(buckets, generation, extractions);\n}\n\n/** Append affected-source changes (logging each addition) to the change list. */\nfunction augmentWithAffectedSources(changes: SourceChange[], affected: string[]): void {\n  for (const file of affected) {\n    output.status(\"~\", output.info(`${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/** Resolve interlinks, regenerate index/MOC, refresh embeddings post-write. */\nasync function finalizeWiki(root: string, pages: MergedConcept[]): Promise<void> {\n  const allChangedSlugs = pages.map((entry) => entry.slug);\n  const allNewSlugs = pages.filter((entry) => entry.concept.is_new).map((entry) => entry.slug);\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 * 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 */\nfunction mergeExtractions(\n  extractions: ExtractionResult[],\n  frozenSlugs: Set<string>,\n): MergedConcept[] {\n  const bySlug = new Map<string, MergedConcept>();\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.sourceFiles.push(result.sourceFile);\n        existing.combinedContent += `\\n\\n--- SOURCE: ${result.sourceFile} ---\\n\\n${result.sourceContent}`;\n      } else {\n        bySlug.set(slug, {\n          slug,\n          concept,\n          sourceFiles: [result.sourceFile],\n          combinedContent: `--- SOURCE: ${result.sourceFile} ---\\n\\n${result.sourceContent}`,\n        });\n      }\n    }\n  }\n\n  return Array.from(bySlug.values());\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.\n */\nasync function generateMergedPage(\n  root: string,\n  entry: MergedConcept,\n): Promise<string | null> {\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 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    createdAt,\n    updatedAt: now,\n  };\n  addObsidianMeta(frontmatterFields, entry.concept.concept, entry.concept.tags ?? []);\n  const frontmatter = buildFrontmatter(frontmatterFields);\n  const fullPage = `${frontmatter}\\n\\n${pageBody}\\n`;\n  return await writePageIfValid(pagePath, fullPage, entry.concept.concept);\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/**\n * Load related wiki pages to provide cross-referencing context.\n * Returns concatenated content of up to 5 existing concept pages.\n * @param root - Project root directory.\n * @param excludeSlug - Slug of the current page to exclude.\n * @returns Concatenated related page contents.\n */\nasync function loadRelatedPages(\n  root: string,\n  excludeSlug: string,\n): 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 !== `${excludeSlug}.md`)\n    .slice(0, 5);\n\n  const contents: string[] = [];\n  for (const f of related) {\n    const content = await safeReadFile(path.join(conceptsPath, f));\n    if (!content) continue;\n    const { meta } = parseFrontmatter(content);\n    if (meta.orphaned) continue;\n    contents.push(content);\n  }\n\n  return contents.join(\"\\n\\n---\\n\\n\");\n}\n\n/**\n * Validate and atomically write a wiki page, logging the result.\n * @param pagePath - Absolute path to write the page.\n * @param content - Full page content including frontmatter.\n * @param conceptTitle - Title for logging purposes.\n */\nasync function writePageIfValid(\n  pagePath: string,\n  content: string,\n  conceptTitle: string,\n): Promise<string | null> {\n  if (!validateWikiPage(content)) {\n    output.status(\"!\", output.warn(`Invalid page for \"${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 type { WikiState, SourceState } from \"./types.js\";\n\nfunction emptyState(): WikiState {\n  return { version: 1, indexHash: \"\", sources: {} };\n}\n\n/** Read .llmwiki/state.json, recovering from corruption gracefully. */\nexport async function readState(root: string): Promise<WikiState> {\n  const filePath = path.join(root, STATE_FILE);\n\n  if (!existsSync(filePath)) {\n    return emptyState();\n  }\n\n  try {\n    const raw = await readFile(filePath, \"utf-8\");\n    return JSON.parse(raw) as WikiState;\n  } catch {\n    const bakPath = filePath + \".bak\";\n    console.warn(`⚠ Corrupt state.json — backed up to ${bakPath}, starting fresh.`);\n    await copyFile(filePath, bakPath);\n    return emptyState();\n  }\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 * 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 { EMBEDDING_MODELS } from \"../utils/constants.js\";\n\nconst VOYAGE_EMBEDDINGS_URL = \"https://api.voyageai.com/v1/embeddings\";\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    });\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    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 ${apiKey}`,\n      },\n      body: JSON.stringify({ input: text, model: EMBEDDING_MODELS.anthropic }),\n    });\n\n    if (!response.ok) {\n      const detail = await response.text();\n      throw new Error(`Voyage embeddings request failed (${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","/**\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 } from \"../utils/constants.js\";\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 model: string;\n\n  constructor(model: string, baseURL?: string, apiKey?: string) {\n    this.model = model;\n    // The OpenAI SDK validates OPENAI_API_KEY at construction time.\n    // Pass the key explicitly so the provider controls when validation happens.\n    const resolvedKey = apiKey ?? process.env.OPENAI_API_KEY ?? \"\";\n    this.client = new OpenAI({\n      apiKey: resolvedKey,\n      ...(baseURL ? { baseURL } : {}),\n    });\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    });\n\n    const toolCalls = response.choices[0]?.message?.tool_calls;\n    if (toolCalls && toolCalls.length > 0) {\n      return toolCalls[0].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.client.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 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 } from \"./openai.js\";\nimport { EMBEDDING_MODELS } from \"../utils/constants.js\";\n\n/** Ollama-backed LLM provider using the OpenAI-compatible endpoint. */\nexport class OllamaProvider extends OpenAIProvider {\n  constructor(model: string, baseURL: string) {\n    super(model, baseURL, \"ollama\");\n  }\n\n  /** Ollama ships a dedicated embedding model (nomic-embed-text). */\n  protected override embeddingModel(): string {\n    return 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, MINIMAX_BASE_URL, apiKey);\n  }\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 * 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 {\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\", \"openai\", \"ollama\", \"minimax\"]);\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 \"openai\":\n      return new OpenAIProvider(getModelForProvider(\"openai\"));\n    case \"ollama\":\n      return new OllamaProvider(\n        getModelForProvider(\"ollama\"),\n        process.env.OLLAMA_HOST ?? OLLAMA_DEFAULT_HOST,\n      );\n    case \"minimax\":\n      return getMiniMaxProvider();\n    default:\n      throw new Error(`Unhandled provider: ${providerName}`);\n  }\n}\n\nfunction getModelForProvider(providerName: \"openai\" | \"ollama\" | \"minimax\"): string {\n  return process.env.LLMWIKI_MODEL ?? PROVIDER_MODELS[providerName];\n}\n\nfunction getMiniMaxProvider(): MiniMaxProvider {\n  const apiKey = process.env.MINIMAX_API_KEY;\n  if (!apiKey) {\n    throw new Error(\n      \"MiniMax provider requires MINIMAX_API_KEY environment variable.\\n\" +\n      '  Set it with: export MINIMAX_API_KEY=your_key',\n    );\n  }\n  return new MiniMaxProvider(getModelForProvider(\"minimax\"), apiKey);\n}\n\nfunction getAnthropicProvider(): AnthropicProvider {\n  const model = resolveAnthropicModelFromEnv() ?? PROVIDER_MODELS.anthropic;\n  const baseURL = resolveAnthropicBaseURLFromEnv();\n  const auth = resolveAnthropicAuthFromEnv();\n\n  return new AnthropicProvider(model, {\n    baseURL,\n    ...auth,\n  });\n}\n\nfunction getProviderName(): string {\n  const providerName = process.env.LLMWIKI_PROVIDER ?? DEFAULT_PROVIDER;\n  if (!SUPPORTED_PROVIDERS.has(providerName)) {\n    throw new Error(\n      `Unknown provider \"${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 * 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\";\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\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) 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      console.warn(`⚠ API call failed (attempt ${attempt + 1}/${RETRY_COUNT + 1}): ${errMsg}`);\n      console.warn(`  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 * 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 { ExtractedConcept } from \"../utils/types.js\";\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          },\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    \"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    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    `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    \"Source attribution: at the end of each prose paragraph, append a citation\",\n    \"marker showing which source file(s) the paragraph drew from.\",\n    \"Format: ^[filename.md] for single-source, ^[source-a.md, source-b.md] for multi-source.\",\n    \"Place citations only at the end of prose paragraphs — not on headings, list items, or code blocks.\",\n    \"Source filenames are visible as `--- SOURCE: filename.md ---` headers in the content below.\",\n    existingSection,\n    relatedSection,\n    \"\\n\\n--- SOURCE MATERIAL ---\\n\\n\",\n    sourceContent,\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: ExtractedConcept[] = parsed.concepts ?? [];\n    return concepts\n      .filter(\n        (c) =>\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      .map((c) => ({\n        concept: c.concept,\n        summary: c.summary,\n        is_new: c.is_new,\n        tags: Array.isArray(c.tags) ? c.tags : undefined,\n      }));\n  } catch {\n    return [];\n  }\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 * 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 [[wikilinks]]. Obsidian-compatible format using\n * display titles, not slugs.\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.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.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.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 * 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  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 title = typeof meta.title === \"string\" ? meta.title : file.replace(/\\.md$/, \"\");\n    const tags = Array.isArray(meta.tags) ? (meta.tags as string[]) : [];\n    pages.push({ 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, string[]> {\n  const groups = new Map<string, string[]>();\n\n  for (const page of pages) {\n    if (page.tags.length === 0) {\n      appendToGroup(groups, \"Uncategorized\", page.title);\n      continue;\n    }\n\n    for (const tag of page.tags) {\n      appendToGroup(groups, tag, page.title);\n    }\n  }\n\n  return groups;\n}\n\n/** Append a title to a group, creating the group if needed. */\nfunction appendToGroup(groups: Map<string, string[]>, key: string, title: string): void {\n  const existing = groups.get(key);\n  if (existing) {\n    existing.push(title);\n  } else {\n    groups.set(key, [title]);\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, string[]>): 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 titles = tagGroups.get(tag) ?? [];\n    lines.push(`## ${tag}`, \"\");\n    for (const title of titles.sort()) {\n      lines.push(`- [[${title}]]`);\n    }\n    lines.push(\"\");\n  }\n\n  return lines.join(\"\\n\");\n}\n","/**\n * Embedding-based semantic search utilities.\n *\n * Maintains a persistent store of page embeddings in .llmwiki/embeddings.json\n * and provides cosine-similarity retrieval so the query command can narrow\n * hundreds of pages down to a small top-K before 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\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 * as output from \"./output.js\";\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/** Root shape of .llmwiki/embeddings.json. */\nexport interface EmbeddingStore {\n  version: 1;\n  model: string;\n  dimensions: number;\n  entries: EmbeddingEntry[];\n}\n\n/** A retrievable page record on disk (concepts/ or queries/). */\ninterface PageRecord {\n  slug: string;\n  title: string;\n  summary: 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/** 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 readEmbeddingStore(root);\n  if (!store || store.entries.length === 0) 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/** 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 content = await safeReadFile(path.join(absDir, file));\n      const { meta } = parseFrontmatter(content);\n      if (meta.orphaned || typeof meta.title !== \"string\") continue;\n      records.push({\n        slug: file.replace(/\\.md$/, \"\"),\n        title: meta.title,\n        summary: typeof meta.summary === \"string\" ? meta.summary : \"\",\n      });\n    }\n  }\n  return records;\n}\n\n/** Build the text that represents a page in the embedding space. */\nfunction buildEmbeddingText(record: PageRecord): string {\n  return record.summary\n    ? `${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/** Choose the active embedding model name, defaulting to anthropic's voyage model. */\nfunction resolveEmbeddingModel(): string {\n  return EMBEDDING_MODELS[getActiveProviderName()] ?? 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 * 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 toEmbed = new Set(changedSlugs.filter((slug) => liveSlugs.has(slug)));\n\n  const existingStore = await readEmbeddingStore(root);\n  const previousEntries = existingStore?.entries ?? [];\n\n  // Cold start: embed every page so the store is immediately useful.\n  if (!existingStore) {\n    for (const record of records) toEmbed.add(record.slug);\n  }\n\n  if (toEmbed.size === 0 && previousEntries.every((e) => liveSlugs.has(e.slug))) {\n    return;\n  }\n\n  const freshEntries = await embedPages(records, toEmbed);\n  const mergedEntries = mergeEntries(previousEntries, freshEntries, liveSlugs);\n\n  const dimensions = mergedEntries[0]?.vector.length ?? 0;\n  const store: EmbeddingStore = {\n    version: 1,\n    model: resolveEmbeddingModel(),\n    dimensions,\n    entries: mergedEntries,\n  };\n  await writeEmbeddingStore(root, store);\n  output.status(\"*\", output.dim(`Embeddings updated (${mergedEntries.length} pages).`));\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 { generateIndex } from \"../compiler/indexgen.js\";\nimport * as output from \"../utils/output.js\";\nimport { QUERY_PAGE_LIMIT, INDEX_FILE, CONCEPTS_DIR, QUERIES_DIR } from \"../utils/constants.js\";\nimport { findRelevantPages, updateEmbeddings } from \"../utils/embeddings.js\";\nimport type { QueryResult } 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} — ${entry.summary}`)\n    .join(\"\\n\");\n}\n\ninterface SelectedPages {\n  pages: string[];\n  rawPages: string[];\n  reasoning: string;\n}\n\n/**\n * Pick relevant pages using embedding pre-filter when available.\n * Falls back to sending the full wiki index when no embeddings store exists\n * or when the embedding call fails.\n */\nasync function selectRelevantPages(root: string, question: string): Promise<SelectedPages> {\n  const candidates = await tryFindRelevantPages(root, question);\n\n  if (candidates.length > 0) {\n    const filteredIndex = buildFilteredIndex(candidates);\n    const { pages: rawPages, reasoning } = await selectPages(question, filteredIndex);\n    // Tool output holds slugs directly in the semantic path — no slugify needed.\n    return { pages: rawPages, rawPages, reasoning };\n  }\n\n  const indexContent = await safeReadFile(path.join(root, INDEX_FILE));\n  const { pages: rawPages, reasoning } = await selectPages(question, indexContent);\n  return { pages: rawPages.map((p) => slugify(p)), rawPages, reasoning };\n}\n\n/** Embedding-based candidate lookup that never throws. */\nasync function tryFindRelevantPages(\n  root: string,\n  question: string,\n): Promise<Array<{ slug: string; title: string; summary: string }>> {\n  try {\n    return await findRelevantPages(root, question);\n  } catch (err) {\n    const message = err instanceof Error ? err.message : String(err);\n    output.status(\"!\", output.dim(`Semantic pre-filter unavailable (${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/** Shared system prompt for the answer-generation step. */\nconst ANSWER_SYSTEM_PROMPT =\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 * Call the LLM with the loaded wiki pages as grounding context.\n * Streams to the provided onToken callback when one is supplied,\n * otherwise returns the full answer without streaming.\n */\nasync function callAnswerLLM(\n  question: string,\n  pagesContent: string,\n  onToken?: (text: string) => void,\n): Promise<string> {\n  const userMessage = `Question: ${question}\\n\\nRelevant wiki pages:\\n${pagesContent}`;\n  return callClaude({\n    system: ANSWER_SYSTEM_PROMPT,\n    messages: [{ role: \"user\", content: userMessage }],\n    stream: Boolean(onToken),\n    onToken,\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}\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 { pages, reasoning } = await selectRelevantPages(root, question);\n  options.onPageSelection?.(pages, reasoning);\n\n  const pagesContent = await loadSelectedPages(root, pages);\n\n  if (!pagesContent) {\n    return { answer: \"\", selectedPages: pages, reasoning };\n  }\n\n  const answer = await callAnswerLLM(question, pagesContent, options.onToken);\n\n  let saved: string | undefined;\n  if (options.save) {\n    saved = await saveQueryPage(root, question, answer);\n  }\n\n  return { answer, selectedPages: pages, reasoning, saved };\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 },\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    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.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 * Commander action for `llmwiki watch`.\n *\n * Monitors sources/ for file changes via chokidar and triggers incremental\n * recompilation automatically. Uses a debounce to batch rapid changes into\n * a single compile pass. Respects the .llmwiki/lock file — queues changes\n * if a compile is already running.\n */\n\nimport { watch as chokidarWatch } from \"chokidar\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport { compile } from \"../compiler/index.js\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\nimport * as output from \"../utils/output.js\";\n\nconst DEBOUNCE_MS = 500;\n\n/**\n * Start watching sources/ for changes and auto-recompile.\n * Runs until the process is killed (Ctrl+C).\n */\nexport default async function watchCommand(): Promise<void> {\n  const sourcesPath = path.resolve(SOURCES_DIR);\n\n  if (!existsSync(sourcesPath)) {\n    output.status(\n      \"!\",\n      output.warn('No sources/ directory found. Run `llmwiki ingest <url>` first.'),\n    );\n    return;\n  }\n\n  output.header(\"llmwiki watch\");\n  output.status(\"👁\", output.info(`Watching ${sourcesPath} for changes...`));\n  output.status(\"i\", output.dim(\"Press Ctrl+C to stop.\\n\"));\n\n  let compiling = false;\n  let pendingRecompile = false;\n  let debounceTimer: ReturnType<typeof setTimeout> | null = null;\n\n  const triggerCompile = async () => {\n    if (compiling) {\n      pendingRecompile = true;\n      return;\n    }\n\n    compiling = true;\n    try {\n      await compile(process.cwd());\n    } catch (err) {\n      const msg = err instanceof Error ? err.message : String(err);\n      output.status(\"!\", output.error(`Compile failed: ${msg}`));\n    }\n\n    compiling = false;\n\n    // If changes arrived during compilation, recompile\n    if (pendingRecompile) {\n      pendingRecompile = false;\n      await triggerCompile();\n    }\n  };\n\n  const scheduleCompile = (eventPath: string, event: string) => {\n    output.status(\n      \"~\",\n      output.dim(`${event}: ${path.basename(eventPath)}`),\n    );\n\n    if (debounceTimer) clearTimeout(debounceTimer);\n    debounceTimer = setTimeout(triggerCompile, DEBOUNCE_MS);\n  };\n\n  const watcher = chokidarWatch(sourcesPath, {\n    ignoreInitial: true,\n    awaitWriteFinish: { stabilityThreshold: 200 },\n  });\n\n  watcher\n    .on(\"add\", (p) => scheduleCompile(p, \"added\"))\n    .on(\"change\", (p) => scheduleCompile(p, \"changed\"))\n    .on(\"unlink\", (p) => scheduleCompile(p, \"deleted\"));\n\n  // Keep process alive\n  await new Promise<void>(() => {});\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 { parseFrontmatter, slugify } from \"../utils/markdown.js\";\nimport { CONCEPTS_DIR, QUERIES_DIR, SOURCES_DIR } from \"../utils/constants.js\";\nimport type { LintResult } from \"./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 */\nasync 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 linkSlug = slugify(captured);\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/** 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 (< ${MIN_BODY_LENGTH} chars)`,\n      });\n    }\n  }\n\n  return results;\n}\n\n/** Find ^[filename.md] citations referencing source files that don't exist. */\nexport async function checkBrokenCitations(root: string): Promise<LintResult[]> {\n  const pages = await collectAllPages(root);\n  const sourcesDir = path.join(root, SOURCES_DIR);\n  const results: LintResult[] = [];\n\n  for (const page of pages) {\n    for (const { captured, line } of findMatchesInContent(page.content, CITATION_PATTERN)) {\n      const citedPath = path.join(sourcesDir, captured);\n      if (!existsSync(citedPath)) {\n        results.push({\n          rule: \"broken-citation\",\n          severity: \"error\",\n          file: page.filePath,\n          message: `Broken citation ^[${captured}] — source file not found`,\n          line,\n        });\n      }\n    }\n  }\n\n  return results;\n}\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 } from \"./types.js\";\nimport {\n  checkBrokenWikilinks,\n  checkOrphanedPages,\n  checkMissingSummaries,\n  checkDuplicateConcepts,\n  checkEmptyPages,\n  checkBrokenCitations,\n} from \"./rules.js\";\n\n/** All lint rules to execute during a lint pass. */\nconst ALL_RULES: LintRule[] = [\n  checkBrokenWikilinks,\n  checkOrphanedPages,\n  checkMissingSummaries,\n  checkDuplicateConcepts,\n  checkEmptyPages,\n  checkBrokenCitations,\n];\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 * @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 ruleResults = await Promise.all(\n    ALL_RULES.map((rule) => rule(root)),\n  );\n\n  const results = ruleResults.flat();\n\n  return {\n    errors: countBySeverity(results, \"error\"),\n    warnings: countBySeverity(results, \"warning\"),\n    info: countBySeverity(results, \"info\"),\n    results,\n  };\n}\n","/**\n * Commander action for `llmwiki lint`.\n *\n * Runs rule-based quality checks against the wiki without any LLM calls.\n * Prints colored diagnostics grouped by severity and exits with code 1\n * if any errors are found.\n */\n\nimport { lint } from \"../linter/index.js\";\nimport * as output from \"../utils/output.js\";\nimport type { LintResult } from \"../linter/types.js\";\n\n/** Map severity levels to output formatting functions. */\nconst SEVERITY_FORMATTERS: Record<LintResult[\"severity\"], (text: string) => string> = {\n  error: output.error,\n  warning: output.warn,\n  info: output.info,\n};\n\n/** Map severity levels to display icons. */\nconst SEVERITY_ICONS: Record<LintResult[\"severity\"], string> = {\n  error: \"x\",\n  warning: \"!\",\n  info: \"i\",\n};\n\n/** Print a single lint result with colored output. */\nfunction printResult(result: LintResult): void {\n  const formatter = SEVERITY_FORMATTERS[result.severity];\n  const icon = SEVERITY_ICONS[result.severity];\n  const location = result.line ? `${result.file}:${result.line}` : result.file;\n  output.status(icon, `${formatter(result.severity)} ${output.dim(location)} ${result.message}`);\n}\n\n/**\n * Run the lint command: execute all rules and print results.\n * Exits with code 1 if any errors are found.\n */\nexport default async function lintCommand(): Promise<void> {\n  output.header(\"Linting wiki\");\n\n  const summary = await lint(process.cwd());\n\n  for (const result of summary.results) {\n    printResult(result);\n  }\n\n  console.log();\n  const summaryLine = [\n    output.error(`${summary.errors} error(s)`),\n    output.warn(`${summary.warnings} warning(s)`),\n    output.info(`${summary.info} info`),\n  ].join(\", \");\n  output.status(\"*\", summaryLine);\n\n  if (summary.errors > 0) {\n    process.exit(1);\n  }\n}\n","/**\n * MCP (Model Context Protocol) server entry point for llmwiki.\n *\n * Exposes llmwiki's automated pipelines (ingest, compile, query, search,\n * lint, read, status) as MCP tools so AI agents can drive the compiler\n * without scraping CLI output. Read-only wiki views are exposed as\n * MCP resources for direct context injection.\n *\n * Transport: stdio. The server reads JSON-RPC messages on stdin and\n * writes responses on stdout, which is the standard surface area for\n * Claude Desktop, Cursor, and other MCP-aware clients.\n */\n\nimport { McpServer } from \"@modelcontextprotocol/sdk/server/mcp.js\";\nimport { StdioServerTransport } from \"@modelcontextprotocol/sdk/server/stdio.js\";\nimport { registerWikiTools } from \"./tools.js\";\nimport { registerWikiResources } from \"./resources.js\";\n\ninterface ServerOptions {\n  /** Project root directory the server operates on. */\n  root: string;\n  /** Server version surfaced to MCP clients in the initialize handshake. */\n  version: string;\n}\n\n/**\n * Start the MCP server bound to stdio transport.\n * Resolves once the transport closes (typically when the parent process exits).\n *\n * @param options - Root directory and server version (the CLI passes its own\n *                  version so the server doesn't need to read package.json).\n */\nexport async function startMCPServer(options: ServerOptions): Promise<void> {\n  const { root, version } = options;\n  const server = new McpServer({ name: \"llmwiki\", version }, {\n    instructions:\n      \"llmwiki is a knowledge compiler. Use ingest_source to add raw sources, \" +\n      \"compile_wiki to run the LLM pipeline, query_wiki for grounded answers, \" +\n      \"and search_pages to retrieve relevant pages. read_page, lint_wiki, and \" +\n      \"wiki_status work without an API key.\",\n  });\n\n  registerWikiTools(server, root);\n  registerWikiResources(server, root);\n\n  const transport = new StdioServerTransport();\n  await server.connect(transport);\n}\n","/**\n * MCP tool registrations for llmwiki.\n *\n * Each tool wraps an existing pipeline function (ingest, compile, query,\n * search, read, lint, status) and converts its structured result into\n * an MCP CallToolResult. Tools that need an LLM provider validate the\n * provider lazily — the server itself starts without credentials so\n * read-only tools always work.\n */\n\nimport path from \"path\";\nimport { z } from \"zod\";\nimport type { McpServer } from \"@modelcontextprotocol/sdk/server/mcp.js\";\nimport { ingestSource } from \"../commands/ingest.js\";\nimport { compileAndReport } from \"../compiler/index.js\";\nimport { generateAnswer, selectPages } from \"../commands/query.js\";\nimport { lint } from \"../linter/index.js\";\nimport { collectPageSummaries, scanWikiPages } from \"../compiler/indexgen.js\";\nimport { detectChanges } from \"../compiler/hasher.js\";\nimport { readState } from \"../utils/state.js\";\nimport { safeReadFile, parseFrontmatter } from \"../utils/markdown.js\";\nimport { findRelevantPages } from \"../utils/embeddings.js\";\nimport {\n  CONCEPTS_DIR,\n  INDEX_FILE,\n  QUERIES_DIR,\n} from \"../utils/constants.js\";\nimport { ensureProviderAvailable } from \"./provider-check.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 search_pages for each matching page. */\ninterface PageRecord {\n  slug: string;\n  title: string;\n  summary: string;\n  body: string;\n}\n\n/**\n * Wrap an arbitrary JSON value as the standard MCP CallToolResult.\n * MCP requires content blocks even for structured payloads, so we mirror\n * the JSON in a text block for clients that don't read structuredContent.\n */\nfunction jsonResult(payload: unknown): {\n  content: Array<{ type: \"text\"; text: string }>;\n  structuredContent: { result: unknown };\n} {\n  return {\n    content: [{ type: \"text\" as const, text: JSON.stringify(payload, null, 2) }],\n    structuredContent: { result: payload },\n  };\n}\n\n/** Register all 7 wiki tools on the given MCP server instance. */\nexport function registerWikiTools(server: McpServer, root: string): void {\n  registerIngestTool(server, root);\n  registerCompileTool(server, root);\n  registerQueryTool(server, root);\n  registerSearchTool(server, root);\n  registerReadTool(server, root);\n  registerLintTool(server, root);\n  registerStatusTool(server, root);\n}\n\nfunction registerIngestTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"ingest_source\",\n    {\n      title: \"Ingest Source\",\n      description:\n        \"Fetch a URL or copy a local file into sources/. Returns the saved filename, \" +\n        \"character count, and whether content was truncated to fit the size limit.\",\n      inputSchema: {\n        source: z\n          .string()\n          .describe(\"URL (http/https) or absolute path to a .md/.txt file\"),\n      },\n    },\n    async ({ source }) => {\n      const previousCwd = process.cwd();\n      try {\n        process.chdir(root);\n        const result = await ingestSource(source);\n        return jsonResult(result);\n      } finally {\n        process.chdir(previousCwd);\n      }\n    },\n  );\n}\n\nfunction registerCompileTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"compile_wiki\",\n    {\n      title: \"Compile Wiki\",\n      description:\n        \"Run the incremental compile pipeline: extract concepts from new/changed \" +\n        \"sources, generate wiki pages, resolve interlinks, and rebuild the index. \" +\n        \"Requires an LLM provider with credentials.\",\n      inputSchema: {},\n    },\n    async () => {\n      ensureProviderAvailable();\n      const result = await compileAndReport(root);\n      return jsonResult(result);\n    },\n  );\n}\n\nfunction registerQueryTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"query_wiki\",\n    {\n      title: \"Query Wiki\",\n      description:\n        \"Ask a natural-language question. Selects relevant pages with the LLM, \" +\n        \"loads them, and returns a grounded answer with citations. Set save=true \" +\n        \"to persist the answer as a wiki page. Requires an LLM provider.\",\n      inputSchema: {\n        question: z.string().describe(\"The natural-language question to answer.\"),\n        save: z\n          .boolean()\n          .optional()\n          .describe(\"Persist the answer as a wiki/queries/ page when true.\"),\n      },\n    },\n    async ({ question, save }) => {\n      ensureProviderAvailable();\n      const result = await generateAnswer(root, question, { save });\n      return jsonResult(result);\n    },\n  );\n}\n\nfunction registerSearchTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"search_pages\",\n    {\n      title: \"Search Pages\",\n      description:\n        \"Select pages relevant to a question and return their full content. \" +\n        \"Uses semantic embeddings when available, falling back to LLM-based \" +\n        \"selection over the wiki index. Requires an LLM provider.\",\n      inputSchema: {\n        question: z.string().describe(\"The query used to rank pages.\"),\n      },\n    },\n    async ({ question }) => {\n      ensureProviderAvailable();\n      const slugs = await pickSearchSlugs(root, question);\n      const records = await loadPageRecords(root, slugs);\n      return jsonResult({ pages: records });\n    },\n  );\n}\n\n/** Resolve search candidates: prefer semantic search, fall back to LLM selection. */\nasync function pickSearchSlugs(root: string, question: string): Promise<string[]> {\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\nfunction registerReadTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"read_page\",\n    {\n      title: \"Read Page\",\n      description:\n        \"Read a single wiki page by slug. Searches concepts/ first, then queries/. \" +\n        \"Returns the parsed frontmatter and body. No LLM call required.\",\n      inputSchema: {\n        slug: z.string().describe(\"Page slug, without .md extension.\"),\n      },\n    },\n    async ({ slug }) => {\n      const page = await readPage(root, slug);\n      if (!page) {\n        throw new Error(`Page not found: ${slug}`);\n      }\n      return jsonResult(page);\n    },\n  );\n}\n\nfunction registerLintTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"lint_wiki\",\n    {\n      title: \"Lint Wiki\",\n      description:\n        \"Run rule-based quality checks (broken wikilinks, orphans, duplicates, \" +\n        \"empty pages, broken citations). Returns structured diagnostics. No LLM call.\",\n      inputSchema: {},\n    },\n    async () => {\n      const summary = await lint(root);\n      return jsonResult(summary);\n    },\n  );\n}\n\nfunction registerStatusTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"wiki_status\",\n    {\n      title: \"Wiki Status\",\n      description:\n        \"Summarize the wiki: page count, source count, last compile time, \" +\n        \"orphaned pages, and pending source changes. Read-only — never \" +\n        \"modifies the workspace.\",\n      inputSchema: {},\n    },\n    async () => jsonResult(await collectStatus(root)),\n  );\n}\n\n/** Read-only status snapshot used by the wiki_status tool. */\nasync function collectStatus(root: string): Promise<WikiStatus> {\n  const concepts = await collectPageSummaries(path.join(root, CONCEPTS_DIR));\n  const queries = await collectPageSummaries(path.join(root, QUERIES_DIR));\n  const state = await readState(root);\n  const changes = await detectChanges(root, state);\n  const orphans = await findOrphanedSlugs(root);\n  const compileTimes = Object.values(state.sources).map((s) => s.compiledAt);\n  const lastCompile = compileTimes.length > 0\n    ? compileTimes.sort().slice(-1)[0]\n    : null;\n\n  return {\n    pages: { concepts: concepts.length, queries: queries.length, total: concepts.length + queries.length },\n    sources: Object.keys(state.sources).length,\n    lastCompiledAt: lastCompile,\n    orphanedPages: orphans,\n    pendingChanges: changes\n      .filter((c) => c.status !== \"unchanged\")\n      .map((c) => ({ file: c.file, status: c.status })),\n  };\n}\n\ninterface WikiStatus {\n  pages: { concepts: number; queries: number; total: number };\n  sources: number;\n  lastCompiledAt: string | null;\n  orphanedPages: string[];\n  pendingChanges: Array<{ file: string; status: string }>;\n}\n\n/** Find concept slugs whose pages are flagged as orphaned. */\nasync function findOrphanedSlugs(root: string): Promise<string[]> {\n  const scanned = await scanWikiPages(path.join(root, CONCEPTS_DIR));\n  return scanned.filter(({ meta }) => meta.orphaned).map(({ slug }) => slug);\n}\n\n/** Load full content for a list of slugs, skipping missing/orphaned pages. */\nasync function loadPageRecords(root: string, slugs: string[]): Promise<PageRecord[]> {\n  const records: PageRecord[] = [];\n  for (const slug of slugs) {\n    const page = await readPage(root, slug);\n    if (page) records.push(page);\n  }\n  return records;\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 */\nexport async function readPage(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","/**\n * Per-tool provider validation for the MCP server.\n *\n * The MCP server starts without any API key check so read-only tools\n * (read_page, lint_wiki, wiki_status) and the ingest tool always work.\n * Tools that need an LLM call (compile, query, search) invoke this guard\n * to surface a clean error if credentials are missing.\n */\n\nimport { DEFAULT_PROVIDER } from \"../utils/constants.js\";\nimport { resolveAnthropicAuthFromEnv } from \"../utils/claude-settings.js\";\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  openai: \"OPENAI_API_KEY\",\n  ollama: null,\n  minimax: \"MINIMAX_API_KEY\",\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 Error(\n        'Anthropic credentials are required for the \"anthropic\" provider. ' +\n          \"Set ANTHROPIC_API_KEY or ANTHROPIC_AUTH_TOKEN.\",\n      );\n    }\n    return;\n  }\n\n  const keyVar = PROVIDER_KEY_VARS[provider];\n  if (keyVar === undefined) {\n    throw new Error(\n      `Unknown provider \"${provider}\". Supported: ${Object.keys(PROVIDER_KEY_VARS).join(\", \")}`,\n    );\n  }\n\n  if (keyVar && !process.env[keyVar]) {\n    throw new Error(\n      `${keyVar} environment variable is required for the \"${provider}\" provider.`,\n    );\n  }\n}\n","/**\n * MCP resource registrations for llmwiki.\n *\n * Resources expose read-only views of the wiki under the llmwiki:// URI\n * scheme. Hosts can attach these as context without invoking a tool —\n * useful for letting agents browse the wiki passively.\n */\n\nimport path from \"path\";\nimport { readdir } from \"fs/promises\";\nimport { McpServer, ResourceTemplate } from \"@modelcontextprotocol/sdk/server/mcp.js\";\nimport {\n  CONCEPTS_DIR,\n  INDEX_FILE,\n  QUERIES_DIR,\n  SOURCES_DIR,\n  STATE_FILE,\n} from \"../utils/constants.js\";\nimport { safeReadFile, parseFrontmatter } from \"../utils/markdown.js\";\nimport { readState } from \"../utils/state.js\";\n\n/** Standard JSON content block for an MCP resource read result. */\nfunction jsonContent(uri: URL, payload: unknown): {\n  uri: string;\n  mimeType: string;\n  text: string;\n} {\n  return {\n    uri: uri.href,\n    mimeType: \"application/json\",\n    text: JSON.stringify(payload, null, 2),\n  };\n}\n\n/** Standard markdown content block for an MCP resource read result. */\nfunction markdownContent(uri: URL, text: string): {\n  uri: string;\n  mimeType: string;\n  text: string;\n} {\n  return {\n    uri: uri.href,\n    mimeType: \"text/markdown\",\n    text,\n  };\n}\n\n/** Register all 5 read-only wiki resources on the given MCP server. */\nexport function registerWikiResources(server: McpServer, root: string): void {\n  registerIndexResource(server, root);\n  registerSourcesResource(server, root);\n  registerStateResource(server, root);\n  registerConceptResource(server, root);\n  registerQueryResource(server, root);\n}\n\nfunction registerIndexResource(server: McpServer, root: string): void {\n  server.registerResource(\n    \"wiki-index\",\n    \"llmwiki://index\",\n    {\n      title: \"Wiki Index\",\n      description: \"Full content of wiki/index.md (auto-generated table of contents).\",\n      mimeType: \"text/markdown\",\n    },\n    async (uri) => {\n      const content = await safeReadFile(path.join(root, INDEX_FILE));\n      return { contents: [markdownContent(uri, content)] };\n    },\n  );\n}\n\nfunction registerSourcesResource(server: McpServer, root: string): void {\n  server.registerResource(\n    \"wiki-sources\",\n    \"llmwiki://sources\",\n    {\n      title: \"Wiki Sources\",\n      description: \"List of ingested source files with frontmatter metadata.\",\n      mimeType: \"application/json\",\n    },\n    async (uri) => ({\n      contents: [jsonContent(uri, await listSources(root))],\n    }),\n  );\n}\n\nfunction registerStateResource(server: McpServer, root: string): void {\n  server.registerResource(\n    \"wiki-state\",\n    \"llmwiki://state\",\n    {\n      title: \"Compilation State\",\n      description: \"Per-source hashes, concepts, and last compile times from .llmwiki/state.json.\",\n      mimeType: \"application/json\",\n    },\n    async (uri) => {\n      const state = await readState(root);\n      return { contents: [jsonContent(uri, state)] };\n    },\n  );\n}\n\nfunction registerConceptResource(server: McpServer, root: string): void {\n  server.registerResource(\n    \"wiki-concept\",\n    new ResourceTemplate(\"llmwiki://concept/{slug}\", {\n      list: async () => listPagesUnder(root, CONCEPTS_DIR, \"concept\"),\n    }),\n    {\n      title: \"Wiki Concept\",\n      description: \"A single concept page from wiki/concepts/ — frontmatter plus body.\",\n      mimeType: \"application/json\",\n    },\n    async (uri, { slug }) => ({\n      contents: [jsonContent(uri, await loadPageWithMeta(root, CONCEPTS_DIR, String(slug)))],\n    }),\n  );\n}\n\nfunction registerQueryResource(server: McpServer, root: string): void {\n  server.registerResource(\n    \"wiki-query\",\n    new ResourceTemplate(\"llmwiki://query/{slug}\", {\n      list: async () => listPagesUnder(root, QUERIES_DIR, \"query\"),\n    }),\n    {\n      title: \"Wiki Query\",\n      description: \"A single saved query page from wiki/queries/ — frontmatter plus body.\",\n      mimeType: \"application/json\",\n    },\n    async (uri, { slug }) => ({\n      contents: [jsonContent(uri, await loadPageWithMeta(root, QUERIES_DIR, String(slug)))],\n    }),\n  );\n}\n\n/** Source listing: filename, frontmatter (truncation, source URL, etc.). */\nasync function listSources(root: string): Promise<Array<Record<string, unknown>>> {\n  const sourcesPath = path.join(root, SOURCES_DIR);\n  let files: string[];\n  try {\n    files = await readdir(sourcesPath);\n  } catch {\n    return [];\n  }\n\n  const records: Array<Record<string, unknown>> = [];\n  for (const file of files.filter((f) => f.endsWith(\".md\"))) {\n    const content = await safeReadFile(path.join(sourcesPath, file));\n    const { meta } = parseFrontmatter(content);\n    records.push({ filename: file, ...meta });\n  }\n  return records;\n}\n\n/** Read a single page and return a structured payload (slug, meta, body). */\nasync function loadPageWithMeta(\n  root: string,\n  dir: string,\n  slug: string,\n): Promise<{ slug: string; meta: Record<string, unknown>; body: string }> {\n  const filePath = path.join(root, dir, `${slug}.md`);\n  const content = await safeReadFile(filePath);\n  if (!content) {\n    throw new Error(`Page not found: ${dir}/${slug}.md`);\n  }\n\n  const { meta, body } = parseFrontmatter(content);\n  return { slug, meta, body: body.trim() };\n}\n\n/** Build a resource list payload by enumerating .md files in a wiki directory. */\nasync function listPagesUnder(\n  root: string,\n  dir: string,\n  scheme: \"concept\" | \"query\",\n): Promise<{ resources: Array<{ uri: string; name: string }> }> {\n  const pagesPath = path.join(root, dir);\n  let files: string[];\n  try {\n    files = await readdir(pagesPath);\n  } catch {\n    return { resources: [] };\n  }\n\n  const resources = files\n    .filter((f) => f.endsWith(\".md\"))\n    .map((f) => {\n      const slug = f.replace(/\\.md$/, \"\");\n      return { uri: `llmwiki://${scheme}/${slug}`, name: slug };\n    });\n\n  return { resources 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+{"version":3,"sources":["../src/cli.ts","../src/commands/ingest.ts","../src/utils/markdown.ts","../src/utils/constants.ts","../src/utils/output.ts","../src/ingest/web.ts","../src/ingest/file.ts","../src/commands/compile.ts","../src/compiler/index.ts","../src/utils/state.ts","../src/compiler/source-state.ts","../src/compiler/hasher.ts","../src/providers/anthropic.ts","../src/providers/openai.ts","../src/providers/ollama.ts","../src/providers/minimax.ts","../src/utils/claude-settings.ts","../src/utils/provider.ts","../src/utils/llm.ts","../src/utils/lock.ts","../src/compiler/prompts.ts","../src/compiler/deps.ts","../src/compiler/orphan.ts","../src/compiler/resolver.ts","../src/compiler/indexgen.ts","../src/compiler/obsidian.ts","../src/utils/embeddings.ts","../src/compiler/candidates.ts","../src/compiler/page-renderer.ts","../src/compiler/provenance.ts","../src/commands/query.ts","../src/commands/watch.ts","../src/linter/rules.ts","../src/linter/index.ts","../src/commands/lint.ts","../src/commands/review-list.ts","../src/commands/review-show.ts","../src/commands/review-approve.ts","../src/commands/review-helpers.ts","../src/commands/review-reject.ts","../src/mcp/server.ts","../src/mcp/tools.ts","../src/mcp/provider-check.ts","../src/mcp/resources.ts"],"sourcesContent":["/**\n * CLI entry point for llmwiki — the knowledge compiler.\n *\n * Registers all commands (ingest, compile, query, watch, lint) via Commander.\n * Validates the correct API key for the selected LLM provider.\n * Designed for `npx llmwiki` or global install via `npm install -g llm-wiki-compiler`.\n */\n\nimport \"dotenv/config\";\nimport { createRequire } from \"module\";\nimport { Command } from \"commander\";\nimport ingestCommand from \"./commands/ingest.js\";\nimport compileCommand from \"./commands/compile.js\";\nimport queryCommand from \"./commands/query.js\";\nimport watchCommand from \"./commands/watch.js\";\nimport lintCommand from \"./commands/lint.js\";\nimport reviewListCommand from \"./commands/review-list.js\";\nimport reviewShowCommand from \"./commands/review-show.js\";\nimport reviewApproveCommand from \"./commands/review-approve.js\";\nimport reviewRejectCommand from \"./commands/review-reject.js\";\nimport { startMCPServer } from \"./mcp/server.js\";\nimport { DEFAULT_PROVIDER } from \"./utils/constants.js\";\nimport { resolveAnthropicAuthFromEnv } from \"./utils/claude-settings.js\";\n\nconst require = createRequire(import.meta.url);\nconst { version } = require(\"../package.json\") as { version: string };\n\nconst program = new Command();\n\nprogram\n  .name(\"llmwiki\")\n  .description(\"The knowledge compiler — raw sources in, interlinked wiki out\")\n  .version(version);\n\nprogram\n  .command(\"ingest <source>\")\n  .description(\"Ingest a URL or local file into sources/\")\n  .action(async (source: string) => {\n    try {\n      await ingestCommand(source);\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"compile\")\n  .description(\"Compile sources/ into an interlinked wiki\")\n  .option(\n    \"--review\",\n    \"Write generated pages as review candidates under .llmwiki/candidates/ instead of mutating wiki/. Orphan-marking for deleted sources is deferred until the next non-review compile.\",\n  )\n  .action(async (options: { review?: boolean }) => {\n    try {\n      requireProvider();\n      await compileCommand({ review: options.review });\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nconst reviewCommand = program\n  .command(\"review\")\n  .description(\"Inspect and act on pending compile review candidates\");\n\nreviewCommand\n  .command(\"list\")\n  .description(\"List pending review candidates\")\n  .action(async () => {\n    try {\n      await reviewListCommand();\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nreviewCommand\n  .command(\"show <id>\")\n  .description(\"Print a single candidate's metadata and body\")\n  .action(async (id: string) => {\n    try {\n      await reviewShowCommand(id);\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nreviewCommand\n  .command(\"approve <id>\")\n  .description(\"Approve a candidate and promote it into wiki/concepts/\")\n  .action(async (id: string) => {\n    try {\n      await reviewApproveCommand(id);\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nreviewCommand\n  .command(\"reject <id>\")\n  .description(\"Reject a candidate and archive it without touching wiki/\")\n  .action(async (id: string) => {\n    try {\n      await reviewRejectCommand(id);\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"query <question>\")\n  .description(\"Ask a question against the wiki\")\n  .option(\"--save\", \"Save the answer as a wiki page\")\n  .action(async (question: string, options: { save?: boolean }) => {\n    try {\n      requireProvider();\n      await queryCommand(process.cwd(), question, options);\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"watch\")\n  .description(\"Watch sources/ and auto-recompile on changes\")\n  .action(async () => {\n    try {\n      requireProvider();\n      await watchCommand();\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"lint\")\n  .description(\"Run rule-based quality checks against the wiki\")\n  .action(async () => {\n    try {\n      await lintCommand();\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\nprogram\n  .command(\"serve\")\n  .description(\"Start an MCP server exposing wiki tools and resources over stdio\")\n  .option(\"--root <dir>\", \"Project root directory\", process.cwd())\n  .action(async (options: { root: string }) => {\n    try {\n      // Per-tool credential checks happen inside the MCP layer so read-only\n      // tools and ingest still work without an API key.\n      await startMCPServer({ root: options.root, version });\n    } catch (err) {\n      console.error(`\\x1b[31mError:\\x1b[0m ${err instanceof Error ? err.message : err}`);\n      process.exit(1);\n    }\n  });\n\n/** API key env var required per provider. Null means no key needed. */\nconst PROVIDER_KEY_VARS: Record<string, string | null> = {\n  anthropic: \"ANTHROPIC_API_KEY\",\n  openai: \"OPENAI_API_KEY\",\n  ollama: null,\n  minimax: \"MINIMAX_API_KEY\",\n};\n\n/** Exit with a helpful message if the selected provider's API key is missing. */\nfunction requireProvider(): void {\n  const provider = process.env.LLMWIKI_PROVIDER ?? DEFAULT_PROVIDER;\n\n  if (provider === \"anthropic\") {\n    const auth = resolveAnthropicAuthFromEnv();\n    if (!auth.apiKey && !auth.authToken) {\n      console.error(\n        `\\x1b[31mError:\\x1b[0m Anthropic credentials are required for the \"anthropic\" provider.\\n` +\n          `  Set one of: export ANTHROPIC_API_KEY=<your-key> OR export ANTHROPIC_AUTH_TOKEN=<your-token>`,\n      );\n      process.exit(1);\n    }\n    return;\n  }\n\n  const keyVar = PROVIDER_KEY_VARS[provider];\n\n  if (keyVar === undefined) {\n    console.error(\n      `\\x1b[31mError:\\x1b[0m Unknown provider \"${provider}\".\\n` +\n        `  Supported: ${Object.keys(PROVIDER_KEY_VARS).join(\", \")}`,\n    );\n    process.exit(1);\n  }\n\n  if (keyVar && !process.env[keyVar]) {\n    console.error(\n      `\\x1b[31mError:\\x1b[0m ${keyVar} environment variable is required for the \"${provider}\" provider.\\n` +\n        `  Set it with: export ${keyVar}=<your-key>`,\n    );\n    process.exit(1);\n  }\n}\n\nprogram.parse();\n","/**\n * Commander action for `llmwiki ingest <source>`.\n * Detects whether the source is a URL or local file, delegates to the\n * appropriate ingestion module, and saves the result as a markdown file\n * with YAML frontmatter in the sources/ directory.\n */\n\nimport path from \"path\";\nimport { mkdir, writeFile } from \"fs/promises\";\nimport { slugify, buildFrontmatter } from \"../utils/markdown.js\";\nimport { MAX_SOURCE_CHARS, MIN_SOURCE_CHARS, SOURCES_DIR } from \"../utils/constants.js\";\nimport * as output from \"../utils/output.js\";\nimport ingestWeb from \"../ingest/web.js\";\nimport ingestFile from \"../ingest/file.js\";\nimport type { IngestResult } 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/** 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 ${MIN_SOURCE_CHARS}).`\n      )\n    );\n  }\n}\n\n/** Build the full markdown document with frontmatter. */\nexport function buildDocument(\n  title: string,\n  source: string,\n  result: TruncateResult,\n): string {\n  const meta: Record<string, unknown> = {\n    title,\n    source,\n    ingestedAt: new Date().toISOString(),\n  };\n  if (result.truncated) {\n    meta.truncated = true;\n    meta.originalChars = result.originalChars;\n  }\n  const frontmatter = buildFrontmatter(meta);\n\n  return `${frontmatter}\\n\\n${result.content}\\n`;\n}\n\n/** Write the ingested document to the sources/ directory. */\nasync function saveSource(title: string, document: string): Promise<string> {\n  const filename = `${slugify(title)}.md`;\n  const destPath = path.join(SOURCES_DIR, filename);\n\n  await mkdir(SOURCES_DIR, { recursive: true });\n  await writeFile(destPath, document, \"utf-8\");\n\n  return destPath;\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) or a local file path (.md or .txt).\n * @returns Saved filename, character count, truncation flag, and source URI.\n */\nexport async function ingestSource(source: string): Promise<IngestResult> {\n  output.status(\"*\", output.info(`Ingesting: ${source}`));\n\n  const { title, content } = isUrl(source)\n    ? await ingestWeb(source)\n    : await ingestFile(source);\n\n  const result = enforceCharLimit(content);\n  enforceMinContent(result.content);\n  const document = buildDocument(title, source, result);\n  const savedPath = await saveSource(title, document);\n\n  return {\n    filename: path.basename(savedPath),\n    charCount: result.content.length,\n    truncated: result.truncated,\n    source,\n  };\n}\n\n/**\n * Ingest a source (URL or local file) and save it to the sources/ directory.\n * @param source - A URL (http/https) or a local file path (.md or .txt).\n */\nexport default async function ingest(source: string): Promise<void> {\n  const result = await ingestSource(source);\n  const savedPath = path.join(SOURCES_DIR, result.filename);\n\n  output.status(\n    \"+\",\n    output.success(`Saved ${output.bold(result.filename)} → ${output.source(savedPath)}`)\n  );\n  output.status(\"→\", output.dim(\"Next: llmwiki compile\"));\n}\n","/**\n * Markdown parsing and manipulation helpers.\n * Handles YAML frontmatter extraction, slugification, and atomic file writes\n * for wiki pages.\n */\n\nimport { writeFile, rename, readFile, mkdir } from \"fs/promises\";\nimport path from \"path\";\nimport yaml from \"js-yaml\";\nimport type { ContradictionRef, ProvenanceState } from \"./types.js\";\n\n/** The set of valid provenance state strings, used to reject unknown values. */\nconst VALID_PROVENANCE_STATES: ReadonlySet<ProvenanceState> = new Set([\n  \"extracted\",\n  \"merged\",\n  \"inferred\",\n  \"ambiguous\",\n]);\n\n/** Provenance metadata parsed from a page's frontmatter. */\ninterface ProvenanceMetadata {\n  confidence?: number;\n  provenanceState?: ProvenanceState;\n  contradictedBy?: ContradictionRef[];\n  inferredParagraphs?: number;\n}\n\n/** Convert a human-readable concept title to a filename slug. */\nexport function slugify(title: string): string {\n  return title\n    .toLowerCase()\n    .replace(/['']/g, \"\")\n    .replace(/[^\\w\\s-]/g, \"\")\n    .replace(/\\s+/g, \"-\")\n    .replace(/-+/g, \"-\")\n    .replace(/^-|-$/g, \"\");\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${dumped}\\n---`;\n}\n\n/** Parse YAML frontmatter from a markdown string. Returns { meta, body }. */\nexport function parseFrontmatter(content: string): {\n  meta: Record<string, unknown>;\n  body: string;\n} {\n  const match = content.match(/^---\\n([\\s\\S]*?)\\n---\\n?([\\s\\S]*)$/);\n  if (!match) {\n    return { meta: {}, body: content };\n  }\n\n  let meta: Record<string, unknown> = {};\n  try {\n    const parsed = yaml.load(match[1]);\n    if (parsed && typeof parsed === \"object\") {\n      meta = parsed as Record<string, unknown>;\n    }\n  } catch {\n    // Malformed YAML — return empty meta so callers degrade gracefully.\n  }\n  return { meta, body: match[2] };\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 single citations (^[source.md]) and multi-source (^[a.md, b.md]).\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 citationPattern = /\\^\\[([^\\]]+)\\]/g;\n  const filenames = new Set<string>();\n\n  let match;\n  while ((match = citationPattern.exec(body)) !== null) {\n    const inner = match[1];\n    for (const part of inner.split(\",\")) {\n      const trimmed = part.trim();\n      if (trimmed.length > 0) {\n        filenames.add(trimmed);\n      }\n    }\n  }\n\n  return [...filenames];\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/** Parse the inferred paragraph count, requiring a non-negative integer. */\nfunction parseInferredParagraphs(raw: unknown): number | undefined {\n  if (typeof raw !== \"number\" || !Number.isInteger(raw) || raw < 0) return undefined;\n  return raw;\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 * @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    inferredParagraphs: parseInferredParagraphs(meta.inferredParagraphs),\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 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/** 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-4-20250514\",\n  openai: \"gpt-4o\",\n  ollama: \"llama3.1\",\n  minimax: \"MiniMax-M2.7\",\n};\n\n/** Default Ollama API base URL. */\nexport const OLLAMA_DEFAULT_HOST = \"http://localhost:11434/v1\";\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\";\nexport const EMBEDDINGS_FILE = \".llmwiki/embeddings.json\";\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/** Number of most similar pages to return from embedding-based pre-filter. */\nexport const EMBEDDING_TOP_K = 15;\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  openai: \"text-embedding-3-small\",\n  ollama: \"nomic-embed-text\",\n};\n","/**\n * ANSI colored terminal output helpers.\n * Provides consistent styling for compilation progress, status messages,\n * and streaming token display.\n */\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}${RESET}`;\n}\n\n/** Print a status line with an icon. */\nexport function status(icon: string, message: string): void {\n  console.log(`${icon} ${message}`);\n}\n\n/** Print a section header. */\nexport function header(title: string): void {\n  console.log(`\\n${BOLD}${title}${RESET}`);\n  console.log(dim(\"─\".repeat(Math.min(title.length + 4, 60))));\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 ${url}`);\n  }\n\n  return {\n    title: article.title || \"Untitled\",\n    htmlContent: article.content,\n  };\n}\n\n/** Convert HTML to clean markdown using Turndown. */\nfunction convertToMarkdown(html: string): string {\n  const turndown = new TurndownService({ headingStyle: \"atx\" });\n  return turndown.turndown(html);\n}\n\n/**\n * Ingest a web URL and return its content as markdown.\n * @param url - The URL to fetch and convert.\n * @returns An object with the extracted title and markdown content.\n * @throws On network failure or unparseable content.\n */\nexport default async function ingestWeb(url: string): Promise<WebIngestResult> {\n  const response = await fetchAndParse(url);\n  const html = await response.text();\n  const { title, htmlContent } = extractReadableContent(html, url);\n  const content = convertToMarkdown(htmlContent);\n\n  return { title, content };\n}\n","/**\n * Local file ingestion module.\n * Reads .md and .txt files from the local filesystem and returns their\n * content as markdown. Markdown files are returned as-is; plain text files\n * are wrapped in a markdown code block. All other extensions are rejected.\n */\n\nimport { readFile } from \"fs/promises\";\nimport path from \"path\";\n\nconst SUPPORTED_EXTENSIONS = new Set([\".md\", \".txt\"]);\n\ninterface FileIngestResult {\n  title: string;\n  content: string;\n}\n\n/** Derive a human-readable title from a filename (without extension). */\nfunction titleFromFilename(filePath: string): string {\n  const basename = path.basename(filePath, path.extname(filePath));\n  return basename.replace(/[-_]+/g, \" \").trim();\n}\n\n/** Wrap plain text content in a markdown fenced block. */\nfunction wrapPlainText(text: string): string {\n  return `\\`\\`\\`\\n${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<FileIngestResult> {\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 * Commander action for `llmwiki compile`.\n * Checks that sources exist, then delegates to the compilation orchestrator\n * to process all new and changed source files into wiki pages.\n */\n\nimport { existsSync } from \"fs\";\nimport { compile } from \"../compiler/index.js\";\nimport * as output from \"../utils/output.js\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\nimport type { CompileOptions } from \"../utils/types.js\";\n\n/**\n * Run the compile command from the current working directory.\n * Exits early if no sources directory exists yet.\n * @param options - Optional behaviour overrides forwarded from the CLI flag set.\n */\nexport default async function compileCommand(options: CompileOptions = {}): Promise<void> {\n  if (!existsSync(SOURCES_DIR)) {\n    output.status(\n      \"!\",\n      output.warn('No sources found. Run `llmwiki ingest <url>` first.'),\n    );\n    return;\n  }\n\n  await compile(process.cwd(), options);\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 } 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  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  parseConcepts,\n} from \"./prompts.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 { generateMOC } from \"./obsidian.js\";\nimport { updateEmbeddings } from \"../utils/embeddings.js\";\nimport { writeCandidate } from \"./candidates.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  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  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\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  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, 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 };\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/** 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  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: generation.pages.map((entry) => entry.slug),\n    errors,\n  };\n  if (options.review) {\n    baseResult.candidates = generation.candidates;\n  }\n  return baseResult;\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 state = await readState(root);\n  const changes = await detectChanges(root, state);\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    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  const generation = await generatePagesPhase(root, extractions, frozenSlugs, 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    await finalizeWiki(root, generation.pages);\n  }\n  return summarizeCompile(buckets, generation, extractions, options);\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/** Resolve interlinks, regenerate index/MOC, refresh embeddings post-write. */\nasync function finalizeWiki(root: string, pages: MergedConcept[]): Promise<void> {\n  const allChangedSlugs = pages.map((entry) => entry.slug);\n  const allNewSlugs = pages.filter((entry) => entry.concept.is_new).map((entry) => entry.slug);\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 * - inferredParagraphs: max (any source claiming inference wins)\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  // Max inferredParagraphs — any source flagging inference raises the count.\n  if (typeof incoming.inferredParagraphs === \"number\") {\n    reconciled.inferredParagraphs = typeof existing.inferredParagraphs === \"number\"\n      ? Math.max(existing.inferredParagraphs, incoming.inferredParagraphs)\n      : incoming.inferredParagraphs;\n  }\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 */\nfunction mergeExtractions(\n  extractions: ExtractionResult[],\n  frozenSlugs: Set<string>,\n): MergedConcept[] {\n  const bySlug = new Map<string, MergedConcept>();\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        existing.combinedContent += `\\n\\n--- SOURCE: ${result.sourceFile} ---\\n\\n${result.sourceContent}`;\n      } else {\n        bySlug.set(slug, {\n          slug,\n          concept,\n          sourceFiles: [result.sourceFile],\n          combinedContent: `--- SOURCE: ${result.sourceFile} ---\\n\\n${result.sourceContent}`,\n        });\n      }\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  options: CompileOptions,\n  sourceStates: SourceStateMap,\n): Promise<MergedPageOutcome> {\n  const fullPage = await renderMergedPageContent(root, entry);\n\n  if (options.review) {\n    return await persistReviewCandidate(root, entry, fullPage, sourceStates);\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): Promise<MergedPageOutcome> {\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  });\n  output.status(\"?\", output.info(`Candidate ready: ${candidate.id} (${entry.slug})`));\n  return { candidateId: candidate.id };\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/**\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 type { WikiState, SourceState } from \"./types.js\";\n\nfunction emptyState(): WikiState {\n  return { version: 1, indexHash: \"\", sources: {} };\n}\n\n/** Read .llmwiki/state.json, recovering from corruption gracefully. */\nexport async function readState(root: string): Promise<WikiState> {\n  const filePath = path.join(root, STATE_FILE);\n\n  if (!existsSync(filePath)) {\n    return emptyState();\n  }\n\n  try {\n    const raw = await readFile(filePath, \"utf-8\");\n    return JSON.parse(raw) as WikiState;\n  } catch {\n    const bakPath = filePath + \".bak\";\n    console.warn(`⚠ Corrupt state.json — backed up to ${bakPath}, starting fresh.`);\n    await copyFile(filePath, bakPath);\n    return emptyState();\n  }\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 * 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 { EMBEDDING_MODELS } from \"../utils/constants.js\";\n\nconst VOYAGE_EMBEDDINGS_URL = \"https://api.voyageai.com/v1/embeddings\";\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    });\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    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 ${apiKey}`,\n      },\n      body: JSON.stringify({ input: text, model: EMBEDDING_MODELS.anthropic }),\n    });\n\n    if (!response.ok) {\n      const detail = await response.text();\n      throw new Error(`Voyage embeddings request failed (${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","/**\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 } 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\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 validates OPENAI_API_KEY at construction time.\n    // Pass the key explicitly so the provider controls when validation happens.\n    const resolvedKey = options.apiKey ?? process.env.OPENAI_API_KEY ?? \"\";\n    this.client = new OpenAI({\n      apiKey: resolvedKey,\n      baseURL: options.baseURL ?? null,\n    });\n    this.embeddingsClient = options.embeddingsBaseURL\n      ? new OpenAI({ apiKey: resolvedKey, baseURL: options.embeddingsBaseURL })\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    });\n\n    const toolCalls = response.choices[0]?.message?.tool_calls;\n    if (toolCalls && toolCalls.length > 0) {\n      return toolCalls[0].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 } from \"./openai.js\";\nimport { EMBEDDING_MODELS } 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\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    });\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 * 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 * 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 {\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\", \"openai\", \"ollama\", \"minimax\"]);\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 \"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    default:\n      throw new Error(`Unhandled provider: ${providerName}`);\n  }\n}\n\nfunction readOptionalEnv(name: string): string | undefined {\n  const value = process.env[name]?.trim();\n  return value ? value : undefined;\n}\n\nfunction getModelForProvider(providerName: \"openai\" | \"ollama\" | \"minimax\"): string {\n  return process.env.LLMWIKI_MODEL ?? PROVIDER_MODELS[providerName];\n}\n\nfunction getMiniMaxProvider(): MiniMaxProvider {\n  const apiKey = process.env.MINIMAX_API_KEY;\n  if (!apiKey) {\n    throw new Error(\n      \"MiniMax provider requires MINIMAX_API_KEY environment variable.\\n\" +\n      '  Set it with: export MINIMAX_API_KEY=your_key',\n    );\n  }\n  return new MiniMaxProvider(getModelForProvider(\"minimax\"), apiKey);\n}\n\nfunction getAnthropicProvider(): AnthropicProvider {\n  const model = resolveAnthropicModelFromEnv() ?? PROVIDER_MODELS.anthropic;\n  const baseURL = resolveAnthropicBaseURLFromEnv();\n  const auth = resolveAnthropicAuthFromEnv();\n\n  return new AnthropicProvider(model, {\n    baseURL,\n    ...auth,\n  });\n}\n\nfunction getProviderName(): string {\n  const providerName = process.env.LLMWIKI_PROVIDER ?? DEFAULT_PROVIDER;\n  if (!SUPPORTED_PROVIDERS.has(providerName)) {\n    throw new Error(\n      `Unknown provider \"${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 * 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\";\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\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) 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      console.warn(`⚠ API call failed (attempt ${attempt + 1}/${RETRY_COUNT + 1}): ${errMsg}`);\n      console.warn(`  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 * 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\";\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            inferred_paragraphs: {\n              type: \"integer\",\n              description:\n                \"Estimated number of paragraphs in the page that will be inferred rather than directly cited.\",\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    \"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    \"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    \"  - inferred_paragraphs: estimated number of paragraphs in the resulting\",\n    \"    page that will be inferred rather than directly citable.\",\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    `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    \"Source attribution: at the end of each prose paragraph, append a citation\",\n    \"marker showing which source file(s) the paragraph drew from.\",\n    \"Format: ^[filename.md] for single-source, ^[source-a.md, source-b.md] for multi-source.\",\n    \"Place citations only at the end of prose paragraphs — not on headings, list items, or code blocks.\",\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    \"to compute the page's provenance metadata.\",\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  inferred_paragraphs?: 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    inferredParagraphs: typeof c.inferred_paragraphs === \"number\" &&\n      Number.isInteger(c.inferred_paragraphs) && c.inferred_paragraphs >= 0\n      ? c.inferred_paragraphs\n      : undefined,\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 * 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 [[wikilinks]]. Obsidian-compatible format using\n * display titles, not slugs.\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.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.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.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 * 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  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 title = typeof meta.title === \"string\" ? meta.title : file.replace(/\\.md$/, \"\");\n    const tags = Array.isArray(meta.tags) ? (meta.tags as string[]) : [];\n    pages.push({ 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, string[]> {\n  const groups = new Map<string, string[]>();\n\n  for (const page of pages) {\n    if (page.tags.length === 0) {\n      appendToGroup(groups, \"Uncategorized\", page.title);\n      continue;\n    }\n\n    for (const tag of page.tags) {\n      appendToGroup(groups, tag, page.title);\n    }\n  }\n\n  return groups;\n}\n\n/** Append a title to a group, creating the group if needed. */\nfunction appendToGroup(groups: Map<string, string[]>, key: string, title: string): void {\n  const existing = groups.get(key);\n  if (existing) {\n    existing.push(title);\n  } else {\n    groups.set(key, [title]);\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, string[]>): 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 titles = tagGroups.get(tag) ?? [];\n    lines.push(`## ${tag}`, \"\");\n    for (const title of titles.sort()) {\n      lines.push(`- [[${title}]]`);\n    }\n    lines.push(\"\");\n  }\n\n  return lines.join(\"\\n\");\n}\n","/**\n * Embedding-based semantic search utilities.\n *\n * Maintains a persistent store of page embeddings in .llmwiki/embeddings.json\n * and provides cosine-similarity retrieval so the query command can narrow\n * hundreds of pages down to a small top-K before 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\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 * as output from \"./output.js\";\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/** Root shape of .llmwiki/embeddings.json. */\nexport interface EmbeddingStore {\n  version: 1;\n  model: string;\n  dimensions: number;\n  entries: EmbeddingEntry[];\n}\n\n/** A retrievable page record on disk (concepts/ or queries/). */\ninterface PageRecord {\n  slug: string;\n  title: string;\n  summary: 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/** 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 readEmbeddingStore(root);\n  if (!store || store.entries.length === 0) return [];\n  const activeModel = resolveEmbeddingModel();\n  if (store.model !== activeModel) {\n    warnStaleEmbeddingStore(store.model, activeModel);\n    return [];\n  }\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/** 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 content = await safeReadFile(path.join(absDir, file));\n      const { meta } = parseFrontmatter(content);\n      if (meta.orphaned || typeof meta.title !== \"string\") continue;\n      records.push({\n        slug: file.replace(/\\.md$/, \"\"),\n        title: meta.title,\n        summary: typeof meta.summary === \"string\" ? meta.summary : \"\",\n      });\n    }\n  }\n  return records;\n}\n\n/** Build the text that represents a page in the embedding space. */\nfunction buildEmbeddingText(record: PageRecord): string {\n  return record.summary\n    ? `${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 * 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\n  // Cold start: embed every page so the store is immediately useful.\n  if (!existingStore || modelChanged) {\n    for (const record of records) toEmbed.add(record.slug);\n  }\n\n  if (!modelChanged && toEmbed.size === 0 && previousEntries.every((e) => liveSlugs.has(e.slug))) {\n    return;\n  }\n\n  const freshEntries = await embedPages(records, toEmbed);\n  const mergedEntries = mergeEntries(previousEntries, freshEntries, liveSlugs);\n\n  const dimensions = mergedEntries[0]?.vector.length ?? 0;\n  const store: EmbeddingStore = {\n    version: 1,\n    model: embeddingModel,\n    dimensions,\n    entries: mergedEntries,\n  };\n  await writeEmbeddingStore(root, store);\n  output.status(\"*\", output.dim(`Embeddings updated (${mergedEntries.length} pages).`));\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 { readdir, rename, unlink, writeFile, mkdir } from \"fs/promises\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport { randomBytes } from \"crypto\";\nimport { atomicWrite, safeReadFile } from \"../utils/markdown.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\";\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\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  };\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  if (!existsSync(dir)) return [];\n\n  const entries = await readdir(dir, { withFileTypes: true });\n  const candidates: ReviewCandidate[] = [];\n  for (const entry of entries) {\n    if (!entry.isFile() || !entry.name.endsWith(CANDIDATE_EXT)) continue;\n    const id = entry.name.slice(0, -CANDIDATE_EXT.length);\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  const sourcePath = candidatePath(root, id);\n  if (!existsSync(sourcePath)) return false;\n\n  const target = archivePath(root, id);\n  await mkdir(path.dirname(target), { recursive: true });\n  // Copy via writeFile + unlink to support cross-filesystem rename failures.\n  try {\n    await rename(sourcePath, target);\n  } catch {\n    const raw = await safeReadFile(sourcePath);\n    await writeFile(target, raw, \"utf-8\");\n    await unlink(sourcePath);\n  }\n  return true;\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 { addProvenanceMeta, reportContradictionWarnings } from \"./provenance.js\";\nimport { CONCEPTS_DIR } from \"../utils/constants.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 * @returns Full markdown content (frontmatter + body, trailing newline).\n */\nexport async function renderMergedPageContent(\n  root: string,\n  entry: RenderableConcept,\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 \"${entry.concept.concept}\".` },\n    ],\n  });\n\n  const frontmatter = buildMergedFrontmatter(entry, existingPage);\n  reportContradictionWarnings(entry.concept.concept, entry.concept);\n  return `${frontmatter}\\n\\n${pageBody}\\n`;\n}\n\n/** Construct the frontmatter block for a merged concept, preserving createdAt. */\nfunction buildMergedFrontmatter(entry: RenderableConcept, existingPage: string): string {\n  const now = new Date().toISOString();\n  const existing = existingPage ? parseFrontmatter(existingPage) : null;\n  const createdAt = (existing?.meta.createdAt && typeof existing.meta.createdAt === \"string\")\n    ? existing.meta.createdAt\n    : now;\n  const frontmatterFields: Record<string, unknown> = {\n    title: entry.concept.concept,\n    summary: entry.concept.summary,\n    sources: entry.sourceFiles,\n    createdAt,\n    updatedAt: now,\n  };\n  addObsidianMeta(frontmatterFields, entry.concept.concept, entry.concept.tags ?? []);\n  addProvenanceMeta(frontmatterFields, entry.concept);\n  return buildFrontmatter(frontmatterFields);\n}\n\n/**\n * Load related wiki pages to provide cross-referencing context.\n * Returns concatenated content of up to RELATED_PAGE_CONTEXT_LIMIT pages.\n * @param root - Project root directory.\n * @param excludeSlug - Slug of the current page to exclude.\n * @returns Concatenated related page contents (empty when concepts dir is missing).\n */\nasync function loadRelatedPages(root: string, excludeSlug: string): Promise<string> {\n  const conceptsPath = path.join(root, CONCEPTS_DIR);\n  let files: string[];\n\n  try {\n    files = await readdir(conceptsPath);\n  } catch {\n    return \"\";\n  }\n\n  const related = files\n    .filter((f) => f.endsWith(\".md\") && f !== `${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 * 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 type { ExtractedConcept } from \"../utils/types.js\";\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  if (typeof concept.inferredParagraphs === \"number\") {\n    fields.inferredParagraphs = concept.inferredParagraphs;\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 * 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 { generateIndex } from \"../compiler/indexgen.js\";\nimport * as output from \"../utils/output.js\";\nimport { QUERY_PAGE_LIMIT, INDEX_FILE, CONCEPTS_DIR, QUERIES_DIR } from \"../utils/constants.js\";\nimport { findRelevantPages, updateEmbeddings } from \"../utils/embeddings.js\";\nimport type { QueryResult } 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} — ${entry.summary}`)\n    .join(\"\\n\");\n}\n\ninterface SelectedPages {\n  pages: string[];\n  rawPages: string[];\n  reasoning: string;\n}\n\n/**\n * Pick relevant pages using embedding pre-filter when available.\n * Falls back to sending the full wiki index when no embeddings store exists\n * or when the embedding call fails.\n */\nasync function selectRelevantPages(root: string, question: string): Promise<SelectedPages> {\n  const candidates = await tryFindRelevantPages(root, question);\n\n  if (candidates.length > 0) {\n    const filteredIndex = buildFilteredIndex(candidates);\n    const { pages: rawPages, reasoning } = await selectPages(question, filteredIndex);\n    // Tool output holds slugs directly in the semantic path — no slugify needed.\n    return { pages: rawPages, rawPages, reasoning };\n  }\n\n  const indexContent = await safeReadFile(path.join(root, INDEX_FILE));\n  const { pages: rawPages, reasoning } = await selectPages(question, indexContent);\n  return { pages: rawPages.map((p) => slugify(p)), rawPages, reasoning };\n}\n\n/** Embedding-based candidate lookup that never throws. */\nasync function tryFindRelevantPages(\n  root: string,\n  question: string,\n): Promise<Array<{ slug: string; title: string; summary: string }>> {\n  try {\n    return await findRelevantPages(root, question);\n  } catch (err) {\n    const message = err instanceof Error ? err.message : String(err);\n    output.status(\"!\", output.dim(`Semantic pre-filter unavailable (${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/** Shared system prompt for the answer-generation step. */\nconst ANSWER_SYSTEM_PROMPT =\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 * Call the LLM with the loaded wiki pages as grounding context.\n * Streams to the provided onToken callback when one is supplied,\n * otherwise returns the full answer without streaming.\n */\nasync function callAnswerLLM(\n  question: string,\n  pagesContent: string,\n  onToken?: (text: string) => void,\n): Promise<string> {\n  const userMessage = `Question: ${question}\\n\\nRelevant wiki pages:\\n${pagesContent}`;\n  return callClaude({\n    system: ANSWER_SYSTEM_PROMPT,\n    messages: [{ role: \"user\", content: userMessage }],\n    stream: Boolean(onToken),\n    onToken,\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}\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 { pages, reasoning } = await selectRelevantPages(root, question);\n  options.onPageSelection?.(pages, reasoning);\n\n  const pagesContent = await loadSelectedPages(root, pages);\n\n  if (!pagesContent) {\n    return { answer: \"\", selectedPages: pages, reasoning };\n  }\n\n  const answer = await callAnswerLLM(question, pagesContent, options.onToken);\n\n  let saved: string | undefined;\n  if (options.save) {\n    saved = await saveQueryPage(root, question, answer);\n  }\n\n  return { answer, selectedPages: pages, reasoning, saved };\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 },\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    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.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 * Commander action for `llmwiki watch`.\n *\n * Monitors sources/ for file changes via chokidar and triggers incremental\n * recompilation automatically. Uses a debounce to batch rapid changes into\n * a single compile pass. Respects the .llmwiki/lock file — queues changes\n * if a compile is already running.\n */\n\nimport { watch as chokidarWatch } from \"chokidar\";\nimport { existsSync } from \"fs\";\nimport path from \"path\";\nimport { compile } from \"../compiler/index.js\";\nimport { SOURCES_DIR } from \"../utils/constants.js\";\nimport * as output from \"../utils/output.js\";\n\nconst DEBOUNCE_MS = 500;\n\n/**\n * Start watching sources/ for changes and auto-recompile.\n * Runs until the process is killed (Ctrl+C).\n */\nexport default async function watchCommand(): Promise<void> {\n  const sourcesPath = path.resolve(SOURCES_DIR);\n\n  if (!existsSync(sourcesPath)) {\n    output.status(\n      \"!\",\n      output.warn('No sources/ directory found. Run `llmwiki ingest <url>` first.'),\n    );\n    return;\n  }\n\n  output.header(\"llmwiki watch\");\n  output.status(\"👁\", output.info(`Watching ${sourcesPath} for changes...`));\n  output.status(\"i\", output.dim(\"Press Ctrl+C to stop.\\n\"));\n\n  let compiling = false;\n  let pendingRecompile = false;\n  let debounceTimer: ReturnType<typeof setTimeout> | null = null;\n\n  const triggerCompile = async () => {\n    if (compiling) {\n      pendingRecompile = true;\n      return;\n    }\n\n    compiling = true;\n    try {\n      await compile(process.cwd());\n    } catch (err) {\n      const msg = err instanceof Error ? err.message : String(err);\n      output.status(\"!\", output.error(`Compile failed: ${msg}`));\n    }\n\n    compiling = false;\n\n    // If changes arrived during compilation, recompile\n    if (pendingRecompile) {\n      pendingRecompile = false;\n      await triggerCompile();\n    }\n  };\n\n  const scheduleCompile = (eventPath: string, event: string) => {\n    output.status(\n      \"~\",\n      output.dim(`${event}: ${path.basename(eventPath)}`),\n    );\n\n    if (debounceTimer) clearTimeout(debounceTimer);\n    debounceTimer = setTimeout(triggerCompile, DEBOUNCE_MS);\n  };\n\n  const watcher = chokidarWatch(sourcesPath, {\n    ignoreInitial: true,\n    awaitWriteFinish: { stabilityThreshold: 200 },\n  });\n\n  watcher\n    .on(\"add\", (p) => scheduleCompile(p, \"added\"))\n    .on(\"change\", (p) => scheduleCompile(p, \"changed\"))\n    .on(\"unlink\", (p) => scheduleCompile(p, \"deleted\"));\n\n  // Keep process alive\n  await new Promise<void>(() => {});\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 { parseFrontmatter, parseProvenanceMetadata, slugify } 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\";\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 */\nasync 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 linkSlug = slugify(captured);\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/** 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/**\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 citations.\n * Uses the metadata-reported count when present and falls back to counting\n * uncited prose paragraphs in the body.\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 { meta, body } = parseFrontmatter(page.content);\n    const provenance = parseProvenanceMetadata(meta);\n    const inferred = provenance.inferredParagraphs ?? 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/** Match a paragraph that looks like prose (not a heading, list, or code block). */\nconst PROSE_PARAGRAPH_LEAD = /^[A-Za-z]/;\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/**\n * Expand a captured citation string into individual source filenames.\n * A multi-source citation like \"a.md, b.md\" is split on commas so each\n * filename can be checked independently. Single-source citations are\n * returned as a one-element array unchanged.\n */\nfunction splitCitationFilenames(captured: string): string[] {\n  return captured.split(\",\").map((s) => s.trim()).filter((s) => s.length > 0);\n}\n\n/** Find ^[filename.md] citations referencing source files that don't exist.\n * Handles both single-source ^[file.md] and multi-source ^[a.md, b.md] forms.\n * Each filename in a multi-source citation is checked independently — only the\n * missing ones are reported, not the entire captured text as one filename.\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\n  for (const page of pages) {\n    for (const { captured, line } of findMatchesInContent(page.content, CITATION_PATTERN)) {\n      for (const filename of splitCitationFilenames(captured)) {\n        const citedPath = path.join(sourcesDir, filename);\n        if (!existsSync(citedPath)) {\n          results.push({\n            rule: \"broken-citation\",\n            severity: \"error\",\n            file: page.filePath,\n            message: `Broken citation ^[${filename}] — source file not found`,\n            line,\n          });\n        }\n      }\n    }\n  }\n\n  return results;\n}\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 } from \"./types.js\";\nimport {\n  checkBrokenWikilinks,\n  checkOrphanedPages,\n  checkMissingSummaries,\n  checkDuplicateConcepts,\n  checkEmptyPages,\n  checkBrokenCitations,\n  checkLowConfidencePages,\n  checkContradictedPages,\n  checkInferredWithoutCitations,\n} from \"./rules.js\";\n\n/** All lint rules to execute during a lint pass. */\nconst ALL_RULES: LintRule[] = [\n  checkBrokenWikilinks,\n  checkOrphanedPages,\n  checkMissingSummaries,\n  checkDuplicateConcepts,\n  checkEmptyPages,\n  checkBrokenCitations,\n  checkLowConfidencePages,\n  checkContradictedPages,\n  checkInferredWithoutCitations,\n];\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 * @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 ruleResults = await Promise.all(\n    ALL_RULES.map((rule) => rule(root)),\n  );\n\n  const results = ruleResults.flat();\n\n  return {\n    errors: countBySeverity(results, \"error\"),\n    warnings: countBySeverity(results, \"warning\"),\n    info: countBySeverity(results, \"info\"),\n    results,\n  };\n}\n","/**\n * Commander action for `llmwiki lint`.\n *\n * Runs rule-based quality checks against the wiki without any LLM calls.\n * Prints colored diagnostics grouped by severity and exits with code 1\n * if any errors are found.\n */\n\nimport { lint } from \"../linter/index.js\";\nimport * as output from \"../utils/output.js\";\nimport type { LintResult } from \"../linter/types.js\";\n\n/** Map severity levels to output formatting functions. */\nconst SEVERITY_FORMATTERS: Record<LintResult[\"severity\"], (text: string) => string> = {\n  error: output.error,\n  warning: output.warn,\n  info: output.info,\n};\n\n/** Map severity levels to display icons. */\nconst SEVERITY_ICONS: Record<LintResult[\"severity\"], string> = {\n  error: \"x\",\n  warning: \"!\",\n  info: \"i\",\n};\n\n/** Print a single lint result with colored output. */\nfunction printResult(result: LintResult): void {\n  const formatter = SEVERITY_FORMATTERS[result.severity];\n  const icon = SEVERITY_ICONS[result.severity];\n  const location = result.line ? `${result.file}:${result.line}` : result.file;\n  output.status(icon, `${formatter(result.severity)} ${output.dim(location)} ${result.message}`);\n}\n\n/**\n * Run the lint command: execute all rules and print results.\n * Exits with code 1 if any errors are found.\n */\nexport default async function lintCommand(): Promise<void> {\n  output.header(\"Linting wiki\");\n\n  const summary = await lint(process.cwd());\n\n  for (const result of summary.results) {\n    printResult(result);\n  }\n\n  console.log();\n  const summaryLine = [\n    output.error(`${summary.errors} error(s)`),\n    output.warn(`${summary.warnings} warning(s)`),\n    output.info(`${summary.info} info`),\n  ].join(\", \");\n  output.status(\"*\", summaryLine);\n\n  if (summary.errors > 0) {\n    process.exit(1);\n  }\n}\n","/**\n * Commander action for `llmwiki review list`.\n *\n * Prints every pending review candidate (id, slug, sources, generated time)\n * so reviewers can pick one to inspect with `llmwiki review show <id>`.\n */\n\nimport { listCandidates } from \"../compiler/candidates.js\";\nimport * as output from \"../utils/output.js\";\n\n/** List every pending candidate from .llmwiki/candidates/. */\nexport default async function reviewListCommand(): Promise<void> {\n  output.header(\"Pending review candidates\");\n\n  const candidates = await listCandidates(process.cwd());\n  if (candidates.length === 0) {\n    output.status(\"✓\", output.success(\"No pending candidates.\"));\n    return;\n  }\n\n  for (const candidate of candidates) {\n    const sources = candidate.sources.join(\", \");\n    const meta = output.dim(`${candidate.generatedAt} | sources: ${sources}`);\n    output.status(\"?\", `${output.info(candidate.id)} → ${candidate.slug} ${meta}`);\n  }\n\n  output.status(\n    \"→\",\n    output.dim(`Use \\`llmwiki review show <id>\\` to inspect a candidate.`),\n  );\n}\n","/**\n * Commander action for `llmwiki review show <id>`.\n *\n * Prints a single candidate's metadata header followed by its full body so\n * reviewers can read the proposed page before approving or rejecting.\n */\n\nimport { loadCandidateOrFail } from \"../compiler/candidates.js\";\nimport * as output from \"../utils/output.js\";\n\n/** Print a single candidate's full content to stdout. */\nexport default async function reviewShowCommand(id: string): Promise<void> {\n  const candidate = await loadCandidateOrFail(process.cwd(), id);\n  if (!candidate) return;\n\n  output.header(`Candidate ${candidate.id}`);\n  output.status(\"i\", output.dim(`title:      ${candidate.title}`));\n  output.status(\"i\", output.dim(`slug:       ${candidate.slug}`));\n  output.status(\"i\", output.dim(`summary:    ${candidate.summary}`));\n  output.status(\"i\", output.dim(`sources:    ${candidate.sources.join(\", \")}`));\n  output.status(\"i\", output.dim(`generated:  ${candidate.generatedAt}`));\n\n  console.log();\n  console.log(candidate.body);\n}\n","/**\n * Commander action for `llmwiki review approve <id>`.\n *\n * Promotes a pending candidate into the live wiki: writes the page body to\n * wiki/concepts/<slug>.md, refreshes the index/MOC, updates embeddings, and\n * removes the candidate file. Approval never re-invokes the LLM — the body\n * stored in the candidate is written verbatim.\n *\n * All mutations are performed under `.llmwiki/lock` to prevent races with a\n * concurrent compile or sibling approve/reject. The candidate is re-read under\n * the lock (TOCTOU guard) — if it disappears between the fast-fail check and\n * lock acquisition (e.g. a concurrent reject ran first), the approval aborts\n * cleanly rather than writing a page from a stale in-memory snapshot.\n */\n\nimport path from \"path\";\nimport {\n  atomicWrite,\n  validateWikiPage,\n} from \"../utils/markdown.js\";\nimport {\n  deleteCandidate,\n  listCandidates,\n} from \"../compiler/candidates.js\";\nimport { generateIndex } from \"../compiler/indexgen.js\";\nimport { generateMOC } from \"../compiler/obsidian.js\";\nimport { resolveLinks } from \"../compiler/resolver.js\";\nimport { updateEmbeddings } from \"../utils/embeddings.js\";\nimport { updateSourceState } from \"../utils/state.js\";\nimport { CONCEPTS_DIR } from \"../utils/constants.js\";\nimport * as output from \"../utils/output.js\";\nimport type { ReviewCandidate } from \"../utils/types.js\";\nimport { runReviewUnderLock, readCandidateUnderLock } from \"./review-helpers.js\";\n\n/** Approve a pending candidate by promoting its body into wiki/concepts/. */\nexport default async function reviewApproveCommand(id: string): Promise<void> {\n  await runReviewUnderLock(id, approveUnderLock);\n}\n\n/**\n * Perform all wiki mutations for an approval while holding the lock.\n *\n * Re-reads the candidate under the lock so that a concurrent reject that ran\n * between the pre-lock fast-fail and lock acquisition is detected. Aborts with\n * exit code 1 if the candidate has disappeared or fails page validation.\n */\nasync function approveUnderLock(root: string, id: string): Promise<void> {\n  const candidate = await readCandidateUnderLock(root, id);\n  if (!candidate) return;\n\n  if (!validateWikiPage(candidate.body)) {\n    output.status(\"!\", output.error(`Candidate ${id} failed page validation; not approved.`));\n    process.exitCode = 1;\n    return;\n  }\n\n  const pagePath = path.join(root, CONCEPTS_DIR, `${candidate.slug}.md`);\n  await atomicWrite(pagePath, candidate.body);\n  output.status(\"+\", output.success(`Approved → ${output.source(pagePath)}`));\n\n  await persistCandidateSourceStates(root, candidate);\n  await refreshWikiAfterApproval(root, candidate.slug);\n  await deleteCandidate(root, id);\n  output.status(\"✓\", output.dim(`Candidate ${id} cleared.`));\n}\n\n/**\n * Flush the source-state snapshot stored on the candidate into\n * `.llmwiki/state.json` so the contributing source files are marked\n * compiled. Without this, approved candidates would re-appear on the next\n * `compile` run because the source still looks \"new\" or \"changed\" to the\n * change detector.\n *\n * When a single source produced multiple candidates (e.g. an extraction\n * yielded several concepts), persisting state on the first approval would\n * mark the source as fully compiled and silently strand the remaining\n * pending candidates — the next `compile --review` would skip the source\n * entirely. To avoid that, we only persist a source's state when no OTHER\n * pending candidate still references that source filename.\n */\nasync function persistCandidateSourceStates(\n  root: string,\n  candidate: ReviewCandidate,\n): Promise<void> {\n  const states = candidate.sourceStates;\n  if (!states) return;\n  const otherSources = await collectOtherCandidateSources(root, candidate.id);\n  for (const [sourceFile, entry] of Object.entries(states)) {\n    if (otherSources.has(sourceFile)) continue;\n    await updateSourceState(root, sourceFile, entry);\n  }\n}\n\n/**\n * Build the set of source filenames referenced by every pending candidate\n * other than the one currently being approved. Used to defer source-state\n * persistence until the LAST candidate from a given source is reviewed.\n */\nasync function collectOtherCandidateSources(\n  root: string,\n  approvingId: string,\n): Promise<Set<string>> {\n  const pending = await listCandidates(root);\n  const sources = new Set<string>();\n  for (const candidate of pending) {\n    if (candidate.id === approvingId) continue;\n    for (const source of candidate.sources) sources.add(source);\n  }\n  return sources;\n}\n\n/** Refresh interlinks, index, MOC, and embeddings after writing a candidate. */\nasync function refreshWikiAfterApproval(root: string, slug: string): Promise<void> {\n  await resolveLinks(root, [slug], [slug]);\n  await generateIndex(root);\n  await generateMOC(root);\n  await safelyUpdateEmbeddings(root, [slug]);\n}\n\n/**\n * Refresh the embeddings store without failing approval.\n * Mirrors the compiler's tolerance: missing API keys / transient provider\n * failures should warn, not abort the approval flow.\n */\nasync function safelyUpdateEmbeddings(root: string, slugs: string[]): Promise<void> {\n  try {\n    await updateEmbeddings(root, slugs);\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 * Shared helpers for review subcommands (approve and reject).\n *\n * Both commands follow the same pattern:\n *   1. Fast-fail: read the candidate before locking (cheap early exit for bad ids).\n *   2. Acquire lock: serialize against concurrent compile / approve / reject.\n *   3. Under-lock re-read: authoritative TOCTOU guard — abort if the candidate\n *      was removed between steps 1 and 2 (e.g. a concurrent reject ran first).\n *   4. Run the mutation.\n *   5. Release lock.\n *\n * Extracting this pattern avoids duplicating the acquire/release boilerplate\n * in both approve and reject.\n */\n\nimport {\n  loadCandidateOrFail,\n  loadCandidateUnderLockOrFail,\n} from \"../compiler/candidates.js\";\nimport { acquireLock, releaseLock } from \"../utils/lock.js\";\nimport * as output from \"../utils/output.js\";\n\n/** Re-export for use by the under-lock mutation functions in approve/reject. */\nexport { loadCandidateUnderLockOrFail as readCandidateUnderLock };\n\n/**\n * Run a review mutation under the `.llmwiki/lock`.\n *\n * Performs the pre-lock fast-fail, acquires the lock, then delegates to the\n * provided `underLock` callback. The lock is released in a `finally` block.\n *\n * @param id - Candidate id to review.\n * @param underLock - Async mutation to run while holding the lock.\n */\nexport async function runReviewUnderLock(\n  id: string,\n  underLock: (root: string, id: string) => Promise<void>,\n): Promise<void> {\n  const root = process.cwd();\n\n  // Fast-fail: surface a clear error for obviously missing ids.\n  // The authoritative check happens under the lock via loadCandidateUnderLockOrFail.\n  const preCheck = await loadCandidateOrFail(root, id);\n  if (!preCheck) return;\n\n  const locked = await acquireLock(root);\n  if (!locked) {\n    output.status(\"!\", output.error(\"Could not acquire lock. Try again later.\"));\n    process.exitCode = 1;\n    return;\n  }\n\n  try {\n    await underLock(root, id);\n  } finally {\n    await releaseLock(root);\n  }\n}\n","/**\n * Commander action for `llmwiki review reject <id>`.\n *\n * Removes a candidate from the pending area without touching `wiki/`.\n * Rejected candidates are moved into .llmwiki/candidates/archive/ so they\n * remain auditable but never appear in `llmwiki review list` again.\n *\n * The archive mutation is performed under `.llmwiki/lock` to serialize\n * concurrent approve/reject and approve-vs-compile operations, matching\n * the lock discipline used by compile and approve.\n *\n * The candidate is re-read under the lock (TOCTOU guard) — if it disappears\n * between the pre-lock fast-fail and lock acquisition, the rejection aborts\n * cleanly rather than silently succeeding on a stale handle.\n */\n\nimport { archiveCandidate } from \"../compiler/candidates.js\";\nimport * as output from \"../utils/output.js\";\nimport { runReviewUnderLock, readCandidateUnderLock } from \"./review-helpers.js\";\n\n/** Reject a pending candidate by archiving its JSON record. */\nexport default async function reviewRejectCommand(id: string): Promise<void> {\n  await runReviewUnderLock(id, rejectUnderLock);\n}\n\n/**\n * Perform the archive mutation while holding the lock.\n *\n * Re-reads the candidate under the lock so that a concurrent approve that ran\n * between the pre-lock fast-fail and lock acquisition is detected. Aborts with\n * exit code 1 if the candidate has disappeared.\n */\nasync function rejectUnderLock(root: string, id: string): Promise<void> {\n  const candidate = await readCandidateUnderLock(root, id);\n  if (!candidate) return;\n\n  await archiveCandidate(root, id);\n  output.status(\n    \"-\",\n    output.warn(`Rejected candidate ${id} (${candidate.slug}) — archived, wiki unchanged.`),\n  );\n}\n","/**\n * MCP (Model Context Protocol) server entry point for llmwiki.\n *\n * Exposes llmwiki's automated pipelines (ingest, compile, query, search,\n * lint, read, status) as MCP tools so AI agents can drive the compiler\n * without scraping CLI output. Read-only wiki views are exposed as\n * MCP resources for direct context injection.\n *\n * Transport: stdio. The server reads JSON-RPC messages on stdin and\n * writes responses on stdout, which is the standard surface area for\n * Claude Desktop, Cursor, and other MCP-aware clients.\n */\n\nimport { McpServer } from \"@modelcontextprotocol/sdk/server/mcp.js\";\nimport { StdioServerTransport } from \"@modelcontextprotocol/sdk/server/stdio.js\";\nimport { registerWikiTools } from \"./tools.js\";\nimport { registerWikiResources } from \"./resources.js\";\n\ninterface ServerOptions {\n  /** Project root directory the server operates on. */\n  root: string;\n  /** Server version surfaced to MCP clients in the initialize handshake. */\n  version: string;\n}\n\n/**\n * Start the MCP server bound to stdio transport.\n * Resolves once the transport closes (typically when the parent process exits).\n *\n * @param options - Root directory and server version (the CLI passes its own\n *                  version so the server doesn't need to read package.json).\n */\nexport async function startMCPServer(options: ServerOptions): Promise<void> {\n  const { root, version } = options;\n  const server = new McpServer({ name: \"llmwiki\", version }, {\n    instructions:\n      \"llmwiki is a knowledge compiler. Use ingest_source to add raw sources, \" +\n      \"compile_wiki to run the LLM pipeline, query_wiki for grounded answers, \" +\n      \"and search_pages to retrieve relevant pages. read_page, lint_wiki, and \" +\n      \"wiki_status work without an API key.\",\n  });\n\n  registerWikiTools(server, root);\n  registerWikiResources(server, root);\n\n  const transport = new StdioServerTransport();\n  await server.connect(transport);\n}\n","/**\n * MCP tool registrations for llmwiki.\n *\n * Each tool wraps an existing pipeline function (ingest, compile, query,\n * search, read, lint, status) and converts its structured result into\n * an MCP CallToolResult. Tools that need an LLM provider validate the\n * provider lazily — the server itself starts without credentials so\n * read-only tools always work.\n */\n\nimport path from \"path\";\nimport { z } from \"zod\";\nimport type { McpServer } from \"@modelcontextprotocol/sdk/server/mcp.js\";\nimport { ingestSource } from \"../commands/ingest.js\";\nimport { compileAndReport } from \"../compiler/index.js\";\nimport { generateAnswer, selectPages } from \"../commands/query.js\";\nimport { lint } from \"../linter/index.js\";\nimport { collectPageSummaries, scanWikiPages } from \"../compiler/indexgen.js\";\nimport { detectChanges } from \"../compiler/hasher.js\";\nimport { countCandidates } from \"../compiler/candidates.js\";\nimport { readState } from \"../utils/state.js\";\nimport { safeReadFile, parseFrontmatter } from \"../utils/markdown.js\";\nimport { findRelevantPages } from \"../utils/embeddings.js\";\nimport {\n  CONCEPTS_DIR,\n  INDEX_FILE,\n  QUERIES_DIR,\n} from \"../utils/constants.js\";\nimport { ensureProviderAvailable } from \"./provider-check.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 search_pages for each matching page. */\ninterface PageRecord {\n  slug: string;\n  title: string;\n  summary: string;\n  body: string;\n}\n\n/**\n * Wrap an arbitrary JSON value as the standard MCP CallToolResult.\n * MCP requires content blocks even for structured payloads, so we mirror\n * the JSON in a text block for clients that don't read structuredContent.\n */\nfunction jsonResult(payload: unknown): {\n  content: Array<{ type: \"text\"; text: string }>;\n  structuredContent: { result: unknown };\n} {\n  return {\n    content: [{ type: \"text\" as const, text: JSON.stringify(payload, null, 2) }],\n    structuredContent: { result: payload },\n  };\n}\n\n/** Register all 7 wiki tools on the given MCP server instance. */\nexport function registerWikiTools(server: McpServer, root: string): void {\n  registerIngestTool(server, root);\n  registerCompileTool(server, root);\n  registerQueryTool(server, root);\n  registerSearchTool(server, root);\n  registerReadTool(server, root);\n  registerLintTool(server, root);\n  registerStatusTool(server, root);\n}\n\nfunction registerIngestTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"ingest_source\",\n    {\n      title: \"Ingest Source\",\n      description:\n        \"Fetch a URL or copy a local file into sources/. Returns the saved filename, \" +\n        \"character count, and whether content was truncated to fit the size limit.\",\n      inputSchema: {\n        source: z\n          .string()\n          .describe(\"URL (http/https) or absolute path to a .md/.txt file\"),\n      },\n    },\n    async ({ source }) => {\n      const previousCwd = process.cwd();\n      try {\n        process.chdir(root);\n        const result = await ingestSource(source);\n        return jsonResult(result);\n      } finally {\n        process.chdir(previousCwd);\n      }\n    },\n  );\n}\n\nfunction registerCompileTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"compile_wiki\",\n    {\n      title: \"Compile Wiki\",\n      description:\n        \"Run the incremental compile pipeline: extract concepts from new/changed \" +\n        \"sources, generate wiki pages, resolve interlinks, and rebuild the index. \" +\n        \"Requires an LLM provider with credentials.\",\n      inputSchema: {},\n    },\n    async () => {\n      ensureProviderAvailable();\n      const result = await compileAndReport(root);\n      return jsonResult(result);\n    },\n  );\n}\n\nfunction registerQueryTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"query_wiki\",\n    {\n      title: \"Query Wiki\",\n      description:\n        \"Ask a natural-language question. Selects relevant pages with the LLM, \" +\n        \"loads them, and returns a grounded answer with citations. Set save=true \" +\n        \"to persist the answer as a wiki page. Requires an LLM provider.\",\n      inputSchema: {\n        question: z.string().describe(\"The natural-language question to answer.\"),\n        save: z\n          .boolean()\n          .optional()\n          .describe(\"Persist the answer as a wiki/queries/ page when true.\"),\n      },\n    },\n    async ({ question, save }) => {\n      ensureProviderAvailable();\n      const result = await generateAnswer(root, question, { save });\n      return jsonResult(result);\n    },\n  );\n}\n\nfunction registerSearchTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"search_pages\",\n    {\n      title: \"Search Pages\",\n      description:\n        \"Select pages relevant to a question and return their full content. \" +\n        \"Uses semantic embeddings when available, falling back to LLM-based \" +\n        \"selection over the wiki index. Requires an LLM provider.\",\n      inputSchema: {\n        question: z.string().describe(\"The query used to rank pages.\"),\n      },\n    },\n    async ({ question }) => {\n      ensureProviderAvailable();\n      const slugs = await pickSearchSlugs(root, question);\n      const records = await loadPageRecords(root, slugs);\n      return jsonResult({ pages: records });\n    },\n  );\n}\n\n/** Resolve search candidates: prefer semantic search, fall back to LLM selection. */\nasync function pickSearchSlugs(root: string, question: string): Promise<string[]> {\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\nfunction registerReadTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"read_page\",\n    {\n      title: \"Read Page\",\n      description:\n        \"Read a single wiki page by slug. Searches concepts/ first, then queries/. \" +\n        \"Returns the parsed frontmatter and body. No LLM call required.\",\n      inputSchema: {\n        slug: z.string().describe(\"Page slug, without .md extension.\"),\n      },\n    },\n    async ({ slug }) => {\n      const page = await readPage(root, slug);\n      if (!page) {\n        throw new Error(`Page not found: ${slug}`);\n      }\n      return jsonResult(page);\n    },\n  );\n}\n\nfunction registerLintTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"lint_wiki\",\n    {\n      title: \"Lint Wiki\",\n      description:\n        \"Run rule-based quality checks (broken wikilinks, orphans, duplicates, \" +\n        \"empty pages, broken citations). Returns structured diagnostics. No LLM call.\",\n      inputSchema: {},\n    },\n    async () => {\n      const summary = await lint(root);\n      return jsonResult(summary);\n    },\n  );\n}\n\nfunction registerStatusTool(server: McpServer, root: string): void {\n  server.registerTool(\n    \"wiki_status\",\n    {\n      title: \"Wiki Status\",\n      description:\n        \"Summarize the wiki: page count, source count, last compile time, \" +\n        \"orphaned pages, and pending source changes. Read-only — never \" +\n        \"modifies the workspace.\",\n      inputSchema: {},\n    },\n    async () => jsonResult(await collectStatus(root)),\n  );\n}\n\n/** Read-only status snapshot used by the wiki_status tool. */\nasync function collectStatus(root: string): Promise<WikiStatus> {\n  const concepts = await collectPageSummaries(path.join(root, CONCEPTS_DIR));\n  const queries = await collectPageSummaries(path.join(root, QUERIES_DIR));\n  const state = await readState(root);\n  const changes = await detectChanges(root, state);\n  const orphans = await findOrphanedSlugs(root);\n  const pendingCandidates = await countCandidates(root);\n  const compileTimes = Object.values(state.sources).map((s) => s.compiledAt);\n  const lastCompile = compileTimes.length > 0\n    ? compileTimes.sort().slice(-1)[0]\n    : null;\n\n  return {\n    pages: { concepts: concepts.length, queries: queries.length, total: concepts.length + queries.length },\n    sources: Object.keys(state.sources).length,\n    lastCompiledAt: lastCompile,\n    orphanedPages: orphans,\n    pendingCandidates,\n    pendingChanges: changes\n      .filter((c) => c.status !== \"unchanged\")\n      .map((c) => ({ file: c.file, status: c.status })),\n  };\n}\n\ninterface WikiStatus {\n  pages: { concepts: number; queries: number; total: number };\n  sources: number;\n  lastCompiledAt: string | null;\n  orphanedPages: string[];\n  /** Number of compile candidates awaiting human review. */\n  pendingCandidates: number;\n  pendingChanges: Array<{ file: string; status: string }>;\n}\n\n/** Find concept slugs whose pages are flagged as orphaned. */\nasync function findOrphanedSlugs(root: string): Promise<string[]> {\n  const scanned = await scanWikiPages(path.join(root, CONCEPTS_DIR));\n  return scanned.filter(({ meta }) => meta.orphaned).map(({ slug }) => slug);\n}\n\n/** Load full content for a list of slugs, skipping missing/orphaned pages. */\nasync function loadPageRecords(root: string, slugs: string[]): Promise<PageRecord[]> {\n  const records: PageRecord[] = [];\n  for (const slug of slugs) {\n    const page = await readPage(root, slug);\n    if (page) records.push(page);\n  }\n  return records;\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 */\nexport async function readPage(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","/**\n * Per-tool provider validation for the MCP server.\n *\n * The MCP server starts without any API key check so read-only tools\n * (read_page, lint_wiki, wiki_status) and the ingest tool always work.\n * Tools that need an LLM call (compile, query, search) invoke this guard\n * to surface a clean error if credentials are missing.\n */\n\nimport { DEFAULT_PROVIDER } from \"../utils/constants.js\";\nimport { resolveAnthropicAuthFromEnv } from \"../utils/claude-settings.js\";\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  openai: \"OPENAI_API_KEY\",\n  ollama: null,\n  minimax: \"MINIMAX_API_KEY\",\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 Error(\n        'Anthropic credentials are required for the \"anthropic\" provider. ' +\n          \"Set ANTHROPIC_API_KEY or ANTHROPIC_AUTH_TOKEN.\",\n      );\n    }\n    return;\n  }\n\n  const keyVar = PROVIDER_KEY_VARS[provider];\n  if (keyVar === undefined) {\n    throw new Error(\n      `Unknown provider \"${provider}\". Supported: ${Object.keys(PROVIDER_KEY_VARS).join(\", \")}`,\n    );\n  }\n\n  if (keyVar && !process.env[keyVar]) {\n    throw new Error(\n      `${keyVar} environment variable is required for the \"${provider}\" provider.`,\n    );\n  }\n}\n","/**\n * MCP resource registrations for llmwiki.\n *\n * Resources expose read-only views of the wiki under the llmwiki:// URI\n * scheme. Hosts can attach these as context without invoking a tool —\n * useful for letting agents browse the wiki passively.\n */\n\nimport path from \"path\";\nimport { readdir } from \"fs/promises\";\nimport { McpServer, ResourceTemplate } from \"@modelcontextprotocol/sdk/server/mcp.js\";\nimport {\n  CONCEPTS_DIR,\n  INDEX_FILE,\n  QUERIES_DIR,\n  SOURCES_DIR,\n  STATE_FILE,\n} from \"../utils/constants.js\";\nimport { safeReadFile, parseFrontmatter } from \"../utils/markdown.js\";\nimport { readState } from \"../utils/state.js\";\n\n/** Standard JSON content block for an MCP resource read result. */\nfunction jsonContent(uri: URL, payload: unknown): {\n  uri: string;\n  mimeType: string;\n  text: string;\n} {\n  return {\n    uri: uri.href,\n    mimeType: \"application/json\",\n    text: JSON.stringify(payload, null, 2),\n  };\n}\n\n/** Standard markdown content block for an MCP resource read result. */\nfunction markdownContent(uri: URL, text: string): {\n  uri: string;\n  mimeType: string;\n  text: string;\n} {\n  return {\n    uri: uri.href,\n    mimeType: \"text/markdown\",\n    text,\n  };\n}\n\n/** Register all 5 read-only wiki resources on the given MCP server. */\nexport function registerWikiResources(server: McpServer, root: string): void {\n  registerIndexResource(server, root);\n  registerSourcesResource(server, root);\n  registerStateResource(server, root);\n  registerConceptResource(server, root);\n  registerQueryResource(server, root);\n}\n\nfunction registerIndexResource(server: McpServer, root: string): void {\n  server.registerResource(\n    \"wiki-index\",\n    \"llmwiki://index\",\n    {\n      title: \"Wiki Index\",\n      description: \"Full content of wiki/index.md (auto-generated table of contents).\",\n      mimeType: \"text/markdown\",\n    },\n    async (uri) => {\n      const content = await safeReadFile(path.join(root, INDEX_FILE));\n      return { contents: [markdownContent(uri, content)] };\n    },\n  );\n}\n\nfunction registerSourcesResource(server: McpServer, root: string): void {\n  server.registerResource(\n    \"wiki-sources\",\n    \"llmwiki://sources\",\n    {\n      title: \"Wiki Sources\",\n      description: \"List of ingested source files with frontmatter metadata.\",\n      mimeType: \"application/json\",\n    },\n    async (uri) => ({\n      contents: [jsonContent(uri, await listSources(root))],\n    }),\n  );\n}\n\nfunction registerStateResource(server: McpServer, root: string): void {\n  server.registerResource(\n    \"wiki-state\",\n    \"llmwiki://state\",\n    {\n      title: \"Compilation State\",\n      description: \"Per-source hashes, concepts, and last compile times from .llmwiki/state.json.\",\n      mimeType: \"application/json\",\n    },\n    async (uri) => {\n      const state = await readState(root);\n      return { contents: [jsonContent(uri, state)] };\n    },\n  );\n}\n\nfunction registerConceptResource(server: McpServer, root: string): void {\n  server.registerResource(\n    \"wiki-concept\",\n    new ResourceTemplate(\"llmwiki://concept/{slug}\", {\n      list: async () => listPagesUnder(root, CONCEPTS_DIR, \"concept\"),\n    }),\n    {\n      title: \"Wiki Concept\",\n      description: \"A single concept page from wiki/concepts/ — frontmatter plus body.\",\n      mimeType: \"application/json\",\n    },\n    async (uri, { slug }) => ({\n      contents: [jsonContent(uri, await loadPageWithMeta(root, CONCEPTS_DIR, String(slug)))],\n    }),\n  );\n}\n\nfunction registerQueryResource(server: McpServer, root: string): void {\n  server.registerResource(\n    \"wiki-query\",\n    new ResourceTemplate(\"llmwiki://query/{slug}\", {\n      list: async () => listPagesUnder(root, QUERIES_DIR, \"query\"),\n    }),\n    {\n      title: \"Wiki Query\",\n      description: \"A single saved query page from wiki/queries/ — frontmatter plus body.\",\n      mimeType: \"application/json\",\n    },\n    async (uri, { slug }) => ({\n      contents: [jsonContent(uri, await loadPageWithMeta(root, QUERIES_DIR, String(slug)))],\n    }),\n  );\n}\n\n/** Source listing: filename, frontmatter (truncation, source URL, etc.). */\nasync function listSources(root: string): Promise<Array<Record<string, unknown>>> {\n  const sourcesPath = path.join(root, SOURCES_DIR);\n  let files: string[];\n  try {\n    files = await readdir(sourcesPath);\n  } catch {\n    return [];\n  }\n\n  const records: Array<Record<string, unknown>> = [];\n  for (const file of files.filter((f) => f.endsWith(\".md\"))) {\n    const content = await safeReadFile(path.join(sourcesPath, file));\n    const { meta } = parseFrontmatter(content);\n    records.push({ filename: file, ...meta });\n  }\n  return records;\n}\n\n/** Read a single page and return a structured payload (slug, meta, body). */\nasync function loadPageWithMeta(\n  root: string,\n  dir: string,\n  slug: string,\n): Promise<{ slug: string; meta: Record<string, unknown>; body: string }> {\n  const filePath = path.join(root, dir, `${slug}.md`);\n  const content = await safeReadFile(filePath);\n  if (!content) {\n    throw new Error(`Page not found: ${dir}/${slug}.md`);\n  }\n\n  const { meta, body } = parseFrontmatter(content);\n  return { slug, meta, body: body.trim() };\n}\n\n/** Build a resource list payload by enumerating .md files in a wiki directory. */\nasync function listPagesUnder(\n  root: string,\n  dir: string,\n  scheme: \"concept\" | \"query\",\n): Promise<{ resources: Array<{ uri: string; name: string }> }> {\n  const pagesPath = path.join(root, dir);\n  let files: string[];\n  try {\n    files = await readdir(pagesPath);\n  } catch {\n    return { resources: [] };\n  }\n\n  const resources = files\n    .filter((f) => f.endsWith(\".md\"))\n    .map((f) => {\n      const slug = f.replace(/\\.md$/, \"\");\n      return { uri: `llmwiki://${scheme}/${slug}`, name: slug };\n    });\n\n  return { resources 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