llm-wiki-compiler 0.1.0 → 0.1.1

package/README.md

@@ -4,6 +4,8 @@ Compile raw sources into an interlinked markdown wiki.
 
 Inspired by Karpathy's [LLM Wiki](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f) pattern: instead of re-discovering knowledge at query time, compile it once into a persistent, browsable artifact that compounds over time.
 
+![llmwiki demo](docs/images/demo.gif)
+
 ## Who this is for
 
 - **AI researchers and engineers** building persistent knowledge from papers, docs, and notes
@@ -97,9 +99,9 @@ Try it on any article or document:
 
 ```bash
 mkdir my-wiki && cd my-wiki
-llmwiki ingest https://en.wikipedia.org/wiki/Knowledge_compilation
+llmwiki ingest https://en.wikipedia.org/wiki/Andrej_Karpathy
 llmwiki compile
-llmwiki query "how does knowledge compilation work?"
+llmwiki query "What terms did Andrej coin?"
 ```
 
 See `examples/basic/` in the repo for pre-generated output you can browse without an API key.

package/dist/cli.js

@@ -82,7 +82,6 @@ var DIM = "\x1B[2m";
 var GREEN = "\x1B[32m";
 var YELLOW = "\x1B[33m";
 var BLUE = "\x1B[34m";
-var MAGENTA = "\x1B[35m";
 var CYAN = "\x1B[36m";
 var RED = "\x1B[31m";
 function bold(text) {
@@ -103,9 +102,6 @@ function info(text) {
 function error(text) {
   return `${RED}${text}${RESET}`;
 }
-function concept(text) {
-  return `${MAGENTA}${BOLD}${text}${RESET}`;
-}
 function source(text) {
   return `${CYAN}${text}${RESET}`;
 }
@@ -526,7 +522,7 @@ ${existingIndex}` : "\n\nNo existing wiki pages yet.";
     sourceContent
   ].join("\n");
 }
-function buildPagePrompt(concept2, sourceContent, existingPage, relatedPages) {
+function buildPagePrompt(concept, sourceContent, existingPage, relatedPages) {
   const existingSection = existingPage ? `
 
 Existing page to update:
@@ -538,7 +534,7 @@ Related wiki pages for cross-referencing:
 
 ${relatedPages}` : "";
   return [
-    `You are a wiki author. Write a clear, well-structured markdown page about "${concept2}".`,
+    `You are a wiki author. Write a clear, well-structured markdown page about "${concept}".`,
     "Draw facts only from the provided source material.",
     "Include a ## Sources section at the end listing the source document.",
     "Suggest [[wikilinks]] to related concepts where appropriate.",
@@ -1036,20 +1032,23 @@ function printChangesSummary(changes) {
   }
 }
 async function extractForSource(root, sourceFile) {
-  header(`Extracting: ${sourceFile}`);
+  status("*", info(`Extracting: ${sourceFile}`));
   const sourcePath = path10.join(root, SOURCES_DIR, sourceFile);
   const sourceContent = await readFile7(sourcePath, "utf-8");
   const existingIndex = await safeReadFile(path10.join(root, INDEX_FILE));
   const concepts = await extractConcepts(sourceContent, existingIndex);
-  if (concepts.length > 0) logExtractedConcepts(concepts);
+  if (concepts.length > 0) {
+    const names = concepts.map((c) => c.concept).join(", ");
+    status("*", dim(`  Found ${concepts.length} concepts: ${names}`));
+  }
   return { sourceFile, sourcePath, sourceContent, concepts };
 }
 function mergeExtractions(extractions, frozenSlugs) {
   const bySlug = /* @__PURE__ */ new Map();
   for (const result of extractions) {
     if (result.concepts.length === 0) continue;
-    for (const concept2 of result.concepts) {
-      const slug = slugify(concept2.concept);
+    for (const concept of result.concepts) {
+      const slug = slugify(concept.concept);
       if (frozenSlugs.has(slug)) continue;
       const existing = bySlug.get(slug);
       if (existing) {
@@ -1062,7 +1061,7 @@ ${result.sourceContent}`;
       } else {
         bySlug.set(slug, {
           slug,
-          concept: concept2,
+          concept,
           sourceFiles: [result.sourceFile],
           combinedContent: `--- SOURCE: ${result.sourceFile} ---
 
@@ -1077,7 +1076,6 @@ async function generateMergedPage(root, entry) {
   const pagePath = path10.join(root, CONCEPTS_DIR, `${entry.slug}.md`);
   const existingPage = await safeReadFile(pagePath);
   const relatedPages = await loadRelatedPages(root, entry.slug);
-  status(">", info(`Generating: ${entry.concept.concept}`));
   const system = buildPagePrompt(
     entry.concept.concept,
     entry.combinedContent,
@@ -1088,11 +1086,8 @@ async function generateMergedPage(root, entry) {
     system,
     messages: [
       { role: "user", content: `Write the wiki page for "${entry.concept.concept}".` }
-    ],
-    stream: true,
-    onToken: (token) => process.stdout.write(dim(token))
+    ]
   });
-  process.stdout.write("\n");
   const now = (/* @__PURE__ */ new Date()).toISOString();
   const existing = existingPage ? parseFrontmatter(existingPage) : null;
   const createdAt = existing?.meta.createdAt && typeof existing.meta.createdAt === "string" ? existing.meta.createdAt : now;
@@ -1110,7 +1105,6 @@ ${pageBody}
   await writePageIfValid(pagePath, fullPage, entry.concept.concept);
 }
 async function extractConcepts(sourceContent, existingIndex) {
-  status("*", info("Extracting concepts..."));
   const system = buildExtractionPrompt(sourceContent, existingIndex);
   const rawOutput = await callClaude({
     system,
@@ -1119,12 +1113,6 @@ async function extractConcepts(sourceContent, existingIndex) {
   });
   return parseConcepts(rawOutput);
 }
-function logExtractedConcepts(concepts) {
-  for (const c of concepts) {
-    const tag = c.is_new ? success("NEW") : dim("update");
-    status("*", `${concept(c.concept)} [${tag}] \u2014 ${c.summary}`);
-  }
-}
 async function loadRelatedPages(root, excludeSlug) {
   const conceptsPath = path10.join(root, CONCEPTS_DIR);
   let files;
@@ -1150,7 +1138,6 @@ async function writePageIfValid(pagePath, content, conceptTitle) {
     return;
   }
   await atomicWrite(pagePath, content);
-  status("+", success(`Wrote: ${conceptTitle}`));
 }
 async function persistSourceState(root, sourcePath, sourceFile, concepts) {
   const hash = await hashFile(sourcePath);

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/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/commands/query.ts","../src/commands/watch.ts"],"sourcesContent":["/**\n * CLI entry point for llmwiki — the knowledge compiler.\n *\n * Registers all commands (ingest, compile, query, watch) via Commander.\n * Validates ANTHROPIC_API_KEY for commands that need LLM access.\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\";\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    requireApiKey();\n    try {\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    requireApiKey();\n    try {\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    requireApiKey();\n    try {\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.parse();\n\n/** Exit with a helpful message if ANTHROPIC_API_KEY is missing. */\nfunction requireApiKey(): void {\n  if (!process.env.ANTHROPIC_API_KEY) {\n    console.error(\n      \"\\x1b[31mError:\\x1b[0m ANTHROPIC_API_KEY environment variable is required.\\n\" +\n        \"  Set it with: export ANTHROPIC_API_KEY=sk-ant-...\\n\" +\n        \"  Get a key at: https://console.anthropic.com/settings/keys\",\n    );\n    process.exit(1);\n  }\n}\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\";\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 * 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  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  output.status(\n    \"+\",\n    output.success(`Saved ${output.bold(title)} → ${output.source(savedPath)}`)\n  );\n  output.status(\"→\", output.dim(\"Next: llmwiki compile\"));\n}\n","/**\n * Markdown parsing and manipulation helpers.\n * Handles YAML frontmatter extraction, slugification, and atomic file writes\n * for wiki pages.\n */\n\nimport { writeFile, rename, readFile, mkdir } from \"fs/promises\";\nimport path from \"path\";\nimport yaml from \"js-yaml\";\n\n/** Convert a human-readable concept title to a filename slug. */\nexport function slugify(title: string): string {\n  return title\n    .toLowerCase()\n    .replace(/['']/g, \"\")\n    .replace(/[^\\w\\s-]/g, \"\")\n    .replace(/\\s+/g, \"-\")\n    .replace(/-+/g, \"-\")\n    .replace(/^-|-$/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/** 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/** Maximum related pages fed as context during page generation. */\nexport const MAX_RELATED_PAGES = 5;\n\n/** API retry configuration. */\nexport const RETRY_COUNT = 3;\nexport const RETRY_BASE_MS = 1000;\nexport const RETRY_MULTIPLIER = 4;\n\n/** Claude model to use for all LLM calls. */\nexport const MODEL = \"claude-sonnet-4-20250514\";\n\n/** Directory names relative to the project root. */\nexport const SOURCES_DIR = \"sources\";\nexport const WIKI_DIR = \"wiki\";\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\";\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 concept(text: string): string {\n  return `${MAGENTA}${BOLD}${text}${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 * 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 { ExtractedConcept, SourceState, SourceChange } from \"../utils/types.js\";\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  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  }\n\n  try {\n    await runCompilePipeline(root);\n  } finally {\n    await releaseLock(root);\n  }\n}\n\n/** Inner pipeline, runs under lock protection. */\nasync function runCompilePipeline(root: string): Promise<void> {\n  const state = await readState(root);\n  const changes = await detectChanges(root, state);\n\n  // Semantic dependency tracking: find unchanged sources that share concepts\n  // with changed sources and need recompilation to preserve cross-source content\n  const affectedFiles = findAffectedSources(state, changes);\n  for (const file of affectedFiles) {\n    output.status(\"~\", output.info(`${file} [affected by shared concept]`));\n    changes.push({ file, status: \"changed\" });\n  }\n\n  const toCompile = changes.filter((c) => c.status === \"new\" || c.status === \"changed\");\n  const deleted = changes.filter((c) => c.status === \"deleted\");\n  const unchanged = changes.filter((c) => c.status === \"unchanged\");\n\n  if (toCompile.length === 0 && deleted.length === 0) {\n    output.status(\"✓\", output.success(\"Nothing to compile — all sources up to date.\"));\n    return;\n  }\n\n  printChangesSummary(changes);\n\n  // Handle deleted sources: mark their wiki pages as orphaned\n  for (const del of deleted) {\n    await markOrphaned(root, del.file, state);\n  }\n\n  // Frozen slugs: shared concepts that lost a contributor (deleted source).\n  const frozenSlugs = findFrozenSlugs(state, changes);\n  for (const slug of frozenSlugs) {\n    output.status(\"i\", output.dim(`Frozen: ${slug} (shared with deleted source)`));\n  }\n\n  // Phase 1: Extract concepts for ALL sources before generating any pages.\n  // This eliminates order-dependence: we know which extractions failed\n  // before committing any page writes.\n  const extractions: ExtractionResult[] = [];\n  for (const change of toCompile) {\n    extractions.push(await extractForSource(root, change.file));\n  }\n\n  // Post-extraction dependency check: new sources may extract concepts\n  // that existing unchanged sources already own. findAffectedSources\n  // couldn't detect this earlier because new sources had no state entry.\n  const lateAffected = findLateAffectedSources(extractions, state, changes);\n  for (const file of lateAffected) {\n    output.status(\"~\", output.info(`${file} [shares concept with new source]`));\n    extractions.push(await extractForSource(root, file));\n  }\n\n  // Freeze concepts from failed extractions before page generation.\n  await freezeFailedExtractions(root, extractions, frozenSlugs);\n\n  // Phase 2: Merge shared concepts across sources, then generate pages.\n  // When multiple sources extract the same concept, combine their content\n  // so the LLM sees all contributing material in a single generation call.\n  const merged = mergeExtractions(extractions, frozenSlugs);\n  const limit = pLimit(COMPILE_CONCURRENCY);\n  const pageResults = await Promise.all(\n    merged.map((entry) => limit(async () => {\n      await generateMergedPage(root, entry);\n      return entry;\n    })),\n  );\n  const allChangedSlugs = pageResults.map((e) => e.slug);\n  const allNewSlugs = pageResults\n    .filter((e) => e.concept.is_new)\n    .map((e) => e.slug);\n\n  // Persist state for each successfully extracted source.\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  // Orphan frozen pages that lost all owners after recompilation.\n  if (frozenSlugs.size > 0) {\n    await orphanUnownedFrozenPages(root, frozenSlugs);\n  }\n\n  // Persist frozen slugs: unfreeze any that are now safe to regenerate\n  // (all current owners compiled and extracted them), keep the rest.\n  await persistFrozenSlugs(root, frozenSlugs, extractions);\n\n  // Interlink resolution: outbound on changed, inbound for new titles\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\n  output.header(\"Compilation complete\");\n  output.status(\"✓\", output.success(\n    `${toCompile.length} compiled, ${unchanged.length} skipped, ${deleted.length} deleted`,\n  ));\n  if (toCompile.length > 0) {\n    output.status(\"→\", output.dim('Next: llmwiki query \"your question here\"'));\n  }\n}\n\n/** Print a summary of detected source file changes. */\nfunction printChangesSummary(changes: SourceChange[]): void {\n  const iconMap: Record<string, string> = {\n    new: \"+\", changed: \"~\", unchanged: \".\", deleted: \"-\",\n  };\n  const fmtMap: Record<string, (s: string) => string> = {\n    new: output.success, changed: output.warn, unchanged: output.dim, deleted: output.error,\n  };\n\n  for (const c of changes) {\n    const icon = iconMap[c.status] ?? \"?\";\n    const fmt = fmtMap[c.status] ?? output.dim;\n    output.status(icon, fmt(`${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.header(`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) logExtractedConcepts(concepts);\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<void> {\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  output.status(\">\", output.info(`Generating: ${entry.concept.concept}`));\n\n  const system = buildPagePrompt(\n    entry.concept.concept,\n    entry.combinedContent,\n    existingPage,\n    relatedPages,\n  );\n\n  const pageBody = await callClaude({\n    system,\n    messages: [\n      { role: \"user\", content: `Write the wiki page for \"${entry.concept.concept}\".` },\n    ],\n    stream: true,\n    onToken: (token) => process.stdout.write(output.dim(token)),\n  });\n\n  process.stdout.write(\"\\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 frontmatter = buildFrontmatter({\n    title: entry.concept.concept,\n    summary: entry.concept.summary,\n    sources: entry.sourceFiles,\n    createdAt,\n    updatedAt: now,\n  });\n  const fullPage = `${frontmatter}\\n\\n${pageBody}\\n`;\n  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  output.status(\"*\", output.info(\"Extracting concepts...\"));\n\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/** Log the list of extracted concepts to the terminal. */\nfunction logExtractedConcepts(\n  concepts: ReturnType<typeof parseConcepts>,\n): void {\n  for (const c of concepts) {\n    const tag = c.is_new ? output.success(\"NEW\") : output.dim(\"update\");\n    output.status(\"*\", `${output.concept(c.concept)} [${tag}] — ${c.summary}`);\n  }\n}\n\n\n/**\n * Load related wiki pages to provide cross-referencing context.\n * Returns concatenated content of up to 5 existing concept pages.\n * @param root - Project root directory.\n * @param excludeSlug - Slug of the current page to exclude.\n * @returns Concatenated related page contents.\n */\nasync function loadRelatedPages(\n  root: string,\n  excludeSlug: string,\n): Promise<string> {\n  const conceptsPath = path.join(root, CONCEPTS_DIR);\n  let files: string[];\n\n  try {\n    files = await readdir(conceptsPath);\n  } catch {\n    return \"\";\n  }\n\n  const related = files\n    .filter((f) => f.endsWith(\".md\") && f !== `${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<void> {\n  if (!validateWikiPage(content)) {\n    output.status(\"!\", output.warn(`Invalid page for \"${conceptTitle}\" — skipped.`));\n    return;\n  }\n\n  await atomicWrite(pagePath, content);\n  output.status(\"+\", output.success(`Wrote: ${conceptTitle}`));\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 * Shared LLM helper wrapping the Anthropic SDK.\n * Provides callClaude() for both streaming and tool_use calls,\n * with retry logic and exponential backoff.\n */\n\nimport Anthropic from \"@anthropic-ai/sdk\";\nimport { MODEL, RETRY_COUNT, RETRY_BASE_MS, RETRY_MULTIPLIER } from \"./constants.js\";\n\nlet client: Anthropic | null = null;\n\n/** Get or create the Anthropic client singleton. */\nexport function getClient(): Anthropic {\n  if (!client) {\n    client = new Anthropic();\n  }\n  return client;\n}\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: Anthropic.MessageParam[];\n  tools?: Anthropic.Tool[];\n  maxTokens?: number;\n  stream?: boolean;\n  onToken?: (text: string) => void;\n}\n\n/**\n * Call Claude with retry logic. Supports both streaming and non-streaming modes.\n * For tool_use calls, returns the parsed tool input. For streaming calls, invokes\n * onToken for each text chunk and returns the full assembled text.\n */\nexport async function callClaude(options: CallClaudeOptions): Promise<string> {\n  const { system, messages, tools, maxTokens = 4096, stream = false, onToken } = options;\n  const anthropic = getClient();\n\n  for (let attempt = 0; attempt <= RETRY_COUNT; attempt++) {\n    try {\n      if (stream) {\n        return await callClaudeStreaming(anthropic, system, messages, maxTokens, onToken);\n      }\n\n      if (tools && tools.length > 0) {\n        return await callClaudeToolUse(anthropic, system, messages, tools, maxTokens);\n      }\n\n      return await callClaudeBasic(anthropic, 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\nasync function callClaudeStreaming(\n  anthropic: Anthropic,\n  system: string,\n  messages: Anthropic.MessageParam[],\n  maxTokens: number,\n  onToken?: (text: string) => void,\n): Promise<string> {\n  const stream = anthropic.messages.stream({\n    model: MODEL,\n    max_tokens: maxTokens,\n    system,\n    messages,\n  });\n\n  let fullText = \"\";\n\n  for await (const event of stream) {\n    if (\n      event.type === \"content_block_delta\" &&\n      event.delta.type === \"text_delta\"\n    ) {\n      fullText += event.delta.text;\n      onToken?.(event.delta.text);\n    }\n  }\n\n  return fullText;\n}\n\nasync function callClaudeToolUse(\n  anthropic: Anthropic,\n  system: string,\n  messages: Anthropic.MessageParam[],\n  tools: Anthropic.Tool[],\n  maxTokens: number,\n): Promise<string> {\n  const response = await anthropic.messages.create({\n    model: MODEL,\n    max_tokens: maxTokens,\n    system,\n    messages,\n    tools,\n  });\n\n  const toolBlock = response.content.find((block) => block.type === \"tool_use\");\n  if (toolBlock && toolBlock.type === \"tool_use\") {\n    return JSON.stringify(toolBlock.input);\n  }\n\n  // Fallback: return text content if no tool use\n  const textBlock = response.content.find((block) => block.type === \"text\");\n  if (textBlock && textBlock.type === \"text\") {\n    return textBlock.text;\n  }\n\n  return \"\";\n}\n\nasync function callClaudeBasic(\n  anthropic: Anthropic,\n  system: string,\n  messages: Anthropic.MessageParam[],\n  maxTokens: number,\n): Promise<string> {\n  const response = await anthropic.messages.create({\n    model: MODEL,\n    max_tokens: maxTokens,\n    system,\n    messages,\n  });\n\n  const textBlock = response.content.find((block) => block.type === \"text\");\n  if (textBlock && textBlock.type === \"text\") {\n    return textBlock.text;\n  }\n\n  return \"\";\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          },\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    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.filter(\n      (c) =>\n        typeof c.concept === \"string\" &&\n        typeof c.summary === \"string\" &&\n        typeof c.is_new === \"boolean\",\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/**\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 = new Set(\n    directChanges\n      .filter((c) => c.status === \"new\" || c.status === \"changed\")\n      .map((c) => c.file),\n  );\n\n  // Deleted files must never be enqueued for recompilation — their source\n  // no longer exists on disk, so compileSource would fail reading it.\n  const deletedFiles = new Set(\n    directChanges\n      .filter((c) => c.status === \"deleted\")\n      .map((c) => c.file),\n  );\n\n  const conceptMap = buildConceptToSourcesMap(state.sources);\n  const affected = new Set<string>();\n\n  for (const changedFile of changedFiles) {\n    const sourceEntry = state.sources[changedFile];\n    if (!sourceEntry) continue;\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 skip = changedFiles.has(contributor)\n          || deletedFiles.has(contributor)\n          || affected.has(contributor);\n        if (!skip) {\n          affected.add(contributor);\n        }\n      }\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 * 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 = new Set(\n    allChanges\n      .filter((c) => c.status === \"new\" || c.status === \"changed\")\n      .map((c) => c.file),\n  );\n  const deletedFiles = new Set(\n    allChanges.filter((c) => c.status === \"deleted\").map((c) => c.file),\n  );\n  const conceptMap = buildConceptToSourcesMap(state.sources);\n\n  // Collect concept slugs from ALL extractions that weren't in the source's\n  // previous concept list. These are \"newly gained\" concepts that\n  // findAffectedSources couldn't have matched pre-extraction.\n  const freshSlugs = new Set<string>();\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)) {\n        freshSlugs.add(slug);\n      }\n    }\n  }\n\n  // Find unchanged sources that own any of those freshly gained slugs.\n  const affected = new Set<string>();\n  for (const slug of freshSlugs) {\n    const owners = conceptMap.get(slug);\n    if (!owners) continue;\n    for (const owner of owners) {\n      if (!compilingFiles.has(owner) && !deletedFiles.has(owner)) {\n        affected.add(owner);\n      }\n    }\n  }\n\n  return Array.from(affected);\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$/, \"\"),\n        title: meta.title,\n        filePath,\n      });\n    }\n  }\n\n  return pages;\n}\n\n/** Check if a position is inside an existing [[wikilink]]. */\nfunction isInsideWikilink(text: string, position: number): boolean {\n  const before = text.lastIndexOf(\"[[\", position);\n  const after = text.indexOf(\"]]\", position);\n  if (before === -1 || after === -1) return false;\n\n  const closeBefore = text.indexOf(\"]]\", before);\n  return closeBefore >= position;\n}\n\n/** Check if a match is at a word boundary. */\nfunction isWordBoundary(text: string, start: number, end: number): boolean {\n  const before = start === 0 || /[\\s,.:;!?()\\[\\]{}/\"']/.test(text[start - 1]);\n  const after = end >= text.length || /[\\s,.:;!?()\\[\\]{}/\"']/.test(text[end]);\n  return before && after;\n}\n\n/**\n * Add [[wikilinks]] to a page's body for any title mentions.\n * Skips already-linked text and non-word-boundary matches.\n */\nfunction addWikilinks(body: string, titles: PageInfo[], selfTitle: string): string {\n  let result = body;\n\n  for (const page of titles) {\n    if (page.title.toLowerCase() === selfTitle.toLowerCase()) continue;\n\n    const escaped = page.title.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n    const regex = new RegExp(escaped, \"gi\");\n    let match;\n\n    // Process matches in reverse to preserve positions\n    const matches: { start: number; end: number }[] = [];\n    while ((match = regex.exec(result)) !== null) {\n      matches.push({ start: match.index, end: match.index + match[0].length });\n    }\n\n    for (const m of matches.reverse()) {\n      if (isInsideWikilink(result, m.start)) continue;\n      if (!isWordBoundary(result, m.start, m.end)) continue;\n\n      result =\n        result.slice(0, m.start) +\n        `[[${page.title}]]` +\n        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 ${total} pages.`));\n}\n\n/**\n * Scan the concepts directory and extract page summaries from frontmatter.\n * @param conceptsPath - Absolute path to wiki/concepts/.\n * @returns Array of page summary objects.\n */\nasync function collectPageSummaries(\n  conceptsPath: string,\n): Promise<PageSummary[]> {\n  let files: string[];\n\n  try {\n    files = await readdir(conceptsPath);\n  } catch {\n    return [];\n  }\n\n  const pages: PageSummary[] = [];\n\n  for (const file of files.filter((f) => f.endsWith(\".md\"))) {\n    const content = await safeReadFile(path.join(conceptsPath, file));\n    const { meta } = parseFrontmatter(content);\n    if (meta.title && typeof meta.title === \"string\" && !meta.orphaned) {\n      pages.push({\n        title: meta.title,\n        slug: file.replace(/\\.md$/, \"\"),\n        summary: typeof meta.summary === \"string\" ? meta.summary : \"\",\n      });\n    }\n  }\n\n  return pages;\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 * 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 Anthropic from \"@anthropic-ai/sdk\";\nimport { callClaude } from \"../utils/llm.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\";\n\n/** Directories to search when loading selected pages, in priority order. */\nconst PAGE_DIRS = [CONCEPTS_DIR, QUERIES_DIR];\n\n/** Anthropic tool schema for page selection. */\nconst PAGE_SELECTION_TOOL: Anthropic.Tool = {\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 */\nasync 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/**\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/**\n * Stream an answer from Claude using the loaded wiki pages as context.\n * @param question - The user's natural language question.\n * @param pagesContent - Combined content of the selected wiki pages.\n * @returns The full answer text after streaming completes.\n */\nasync function streamAnswer(question: string, pagesContent: string): Promise<string> {\n  const systemPrompt =\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  const userMessage = `Question: ${question}\\n\\nRelevant wiki pages:\\n${pagesContent}`;\n\n  const answer = await callClaude({\n    system: systemPrompt,\n    messages: [{ role: \"user\", content: userMessage }],\n    stream: true,\n    onToken: (text: string) => process.stdout.write(text),\n  });\n\n  // Ensure terminal output ends on a new line after streaming\n  process.stdout.write(\"\\n\");\n  return answer;\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<void> {\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\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  // Step 1: Select relevant pages\n  output.header(\"Selecting relevant pages\");\n\n  const indexContent = await safeReadFile(path.join(root, INDEX_FILE));\n  const { pages: rawPages, reasoning } = await selectPages(question, indexContent);\n  const pages = rawPages.map((p) => slugify(p));\n\n  output.status(\"i\", output.dim(`Reasoning: ${reasoning}`));\n  output.status(\"*\", output.info(`Selected ${pages.length} page(s): ${rawPages.join(\", \")}`));\n\n  // Step 2: Load pages and stream the answer\n  output.header(\"Generating answer\");\n\n  const pagesContent = await loadSelectedPages(root, pages);\n\n  if (!pagesContent) {\n    output.status(\"!\", output.error(\"No matching pages found. Try refining your question.\"));\n    return;\n  }\n\n  const answer = await streamAnswer(question, pagesContent);\n\n  // Optional: save the answer as a query page\n  if (options.save) {\n    await saveQueryPage(root, question, answer);\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>(() => 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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/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/commands/query.ts","../src/commands/watch.ts"],"sourcesContent":["/**\n * CLI entry point for llmwiki — the knowledge compiler.\n *\n * Registers all commands (ingest, compile, query, watch) via Commander.\n * Validates ANTHROPIC_API_KEY for commands that need LLM access.\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\";\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    requireApiKey();\n    try {\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    requireApiKey();\n    try {\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    requireApiKey();\n    try {\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.parse();\n\n/** Exit with a helpful message if ANTHROPIC_API_KEY is missing. */\nfunction requireApiKey(): void {\n  if (!process.env.ANTHROPIC_API_KEY) {\n    console.error(\n      \"\\x1b[31mError:\\x1b[0m ANTHROPIC_API_KEY environment variable is required.\\n\" +\n        \"  Set it with: export ANTHROPIC_API_KEY=sk-ant-...\\n\" +\n        \"  Get a key at: https://console.anthropic.com/settings/keys\",\n    );\n    process.exit(1);\n  }\n}\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\";\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 * 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  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  output.status(\n    \"+\",\n    output.success(`Saved ${output.bold(title)} → ${output.source(savedPath)}`)\n  );\n  output.status(\"→\", output.dim(\"Next: llmwiki compile\"));\n}\n","/**\n * Markdown parsing and manipulation helpers.\n * Handles YAML frontmatter extraction, slugification, and atomic file writes\n * for wiki pages.\n */\n\nimport { writeFile, rename, readFile, mkdir } from \"fs/promises\";\nimport path from \"path\";\nimport yaml from \"js-yaml\";\n\n/** Convert a human-readable concept title to a filename slug. */\nexport function slugify(title: string): string {\n  return title\n    .toLowerCase()\n    .replace(/['']/g, \"\")\n    .replace(/[^\\w\\s-]/g, \"\")\n    .replace(/\\s+/g, \"-\")\n    .replace(/-+/g, \"-\")\n    .replace(/^-|-$/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/** 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/** Maximum related pages fed as context during page generation. */\nexport const MAX_RELATED_PAGES = 5;\n\n/** API retry configuration. */\nexport const RETRY_COUNT = 3;\nexport const RETRY_BASE_MS = 1000;\nexport const RETRY_MULTIPLIER = 4;\n\n/** Claude model to use for all LLM calls. */\nexport const MODEL = \"claude-sonnet-4-20250514\";\n\n/** Directory names relative to the project root. */\nexport const SOURCES_DIR = \"sources\";\nexport const WIKI_DIR = \"wiki\";\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\";\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 concept(text: string): string {\n  return `${MAGENTA}${BOLD}${text}${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 * 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 { ExtractedConcept, SourceState, SourceChange } from \"../utils/types.js\";\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  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  }\n\n  try {\n    await runCompilePipeline(root);\n  } finally {\n    await releaseLock(root);\n  }\n}\n\n/** Inner pipeline, runs under lock protection. */\nasync function runCompilePipeline(root: string): Promise<void> {\n  const state = await readState(root);\n  const changes = await detectChanges(root, state);\n\n  // Semantic dependency tracking: find unchanged sources that share concepts\n  // with changed sources and need recompilation to preserve cross-source content\n  const affectedFiles = findAffectedSources(state, changes);\n  for (const file of affectedFiles) {\n    output.status(\"~\", output.info(`${file} [affected by shared concept]`));\n    changes.push({ file, status: \"changed\" });\n  }\n\n  const toCompile = changes.filter((c) => c.status === \"new\" || c.status === \"changed\");\n  const deleted = changes.filter((c) => c.status === \"deleted\");\n  const unchanged = changes.filter((c) => c.status === \"unchanged\");\n\n  if (toCompile.length === 0 && deleted.length === 0) {\n    output.status(\"✓\", output.success(\"Nothing to compile — all sources up to date.\"));\n    return;\n  }\n\n  printChangesSummary(changes);\n\n  // Handle deleted sources: mark their wiki pages as orphaned\n  for (const del of deleted) {\n    await markOrphaned(root, del.file, state);\n  }\n\n  // Frozen slugs: shared concepts that lost a contributor (deleted source).\n  const frozenSlugs = findFrozenSlugs(state, changes);\n  for (const slug of frozenSlugs) {\n    output.status(\"i\", output.dim(`Frozen: ${slug} (shared with deleted source)`));\n  }\n\n  // Phase 1: Extract concepts for ALL sources before generating any pages.\n  // This eliminates order-dependence: we know which extractions failed\n  // before committing any page writes.\n  const extractions: ExtractionResult[] = [];\n  for (const change of toCompile) {\n    extractions.push(await extractForSource(root, change.file));\n  }\n\n  // Post-extraction dependency check: new sources may extract concepts\n  // that existing unchanged sources already own. findAffectedSources\n  // couldn't detect this earlier because new sources had no state entry.\n  const lateAffected = findLateAffectedSources(extractions, state, changes);\n  for (const file of lateAffected) {\n    output.status(\"~\", output.info(`${file} [shares concept with new source]`));\n    extractions.push(await extractForSource(root, file));\n  }\n\n  // Freeze concepts from failed extractions before page generation.\n  await freezeFailedExtractions(root, extractions, frozenSlugs);\n\n  // Phase 2: Merge shared concepts across sources, then generate pages.\n  // When multiple sources extract the same concept, combine their content\n  // so the LLM sees all contributing material in a single generation call.\n  const merged = mergeExtractions(extractions, frozenSlugs);\n  const limit = pLimit(COMPILE_CONCURRENCY);\n  const pageResults = await Promise.all(\n    merged.map((entry) => limit(async () => {\n      await generateMergedPage(root, entry);\n      return entry;\n    })),\n  );\n  const allChangedSlugs = pageResults.map((e) => e.slug);\n  const allNewSlugs = pageResults\n    .filter((e) => e.concept.is_new)\n    .map((e) => e.slug);\n\n  // Persist state for each successfully extracted source.\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  // Orphan frozen pages that lost all owners after recompilation.\n  if (frozenSlugs.size > 0) {\n    await orphanUnownedFrozenPages(root, frozenSlugs);\n  }\n\n  // Persist frozen slugs: unfreeze any that are now safe to regenerate\n  // (all current owners compiled and extracted them), keep the rest.\n  await persistFrozenSlugs(root, frozenSlugs, extractions);\n\n  // Interlink resolution: outbound on changed, inbound for new titles\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\n  output.header(\"Compilation complete\");\n  output.status(\"✓\", output.success(\n    `${toCompile.length} compiled, ${unchanged.length} skipped, ${deleted.length} deleted`,\n  ));\n  if (toCompile.length > 0) {\n    output.status(\"→\", output.dim('Next: llmwiki query \"your question here\"'));\n  }\n}\n\n/** Print a summary of detected source file changes. */\nfunction printChangesSummary(changes: SourceChange[]): void {\n  const iconMap: Record<string, string> = {\n    new: \"+\", changed: \"~\", unchanged: \".\", deleted: \"-\",\n  };\n  const fmtMap: Record<string, (s: string) => string> = {\n    new: output.success, changed: output.warn, unchanged: output.dim, deleted: output.error,\n  };\n\n  for (const c of changes) {\n    const icon = iconMap[c.status] ?? \"?\";\n    const fmt = fmtMap[c.status] ?? output.dim;\n    output.status(icon, fmt(`${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<void> {\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 frontmatter = buildFrontmatter({\n    title: entry.concept.concept,\n    summary: entry.concept.summary,\n    sources: entry.sourceFiles,\n    createdAt,\n    updatedAt: now,\n  });\n  const fullPage = `${frontmatter}\\n\\n${pageBody}\\n`;\n  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 !== `${excludeSlug}.md`)\n    .slice(0, 5);\n\n  const contents: string[] = [];\n  for (const f of related) {\n    const content = await safeReadFile(path.join(conceptsPath, f));\n    if (!content) continue;\n    const { meta } = parseFrontmatter(content);\n    if (meta.orphaned) continue;\n    contents.push(content);\n  }\n\n  return contents.join(\"\\n\\n---\\n\\n\");\n}\n\n/**\n * Validate and atomically write a wiki page, logging the result.\n * @param pagePath - Absolute path to write the page.\n * @param content - Full page content including frontmatter.\n * @param conceptTitle - Title for logging purposes.\n */\nasync function writePageIfValid(\n  pagePath: string,\n  content: string,\n  conceptTitle: string,\n): Promise<void> {\n  if (!validateWikiPage(content)) {\n    output.status(\"!\", output.warn(`Invalid page for \"${conceptTitle}\" — skipped.`));\n    return;\n  }\n\n  await atomicWrite(pagePath, content);\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 * Shared LLM helper wrapping the Anthropic SDK.\n * Provides callClaude() for both streaming and tool_use calls,\n * with retry logic and exponential backoff.\n */\n\nimport Anthropic from \"@anthropic-ai/sdk\";\nimport { MODEL, RETRY_COUNT, RETRY_BASE_MS, RETRY_MULTIPLIER } from \"./constants.js\";\n\nlet client: Anthropic | null = null;\n\n/** Get or create the Anthropic client singleton. */\nexport function getClient(): Anthropic {\n  if (!client) {\n    client = new Anthropic();\n  }\n  return client;\n}\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: Anthropic.MessageParam[];\n  tools?: Anthropic.Tool[];\n  maxTokens?: number;\n  stream?: boolean;\n  onToken?: (text: string) => void;\n}\n\n/**\n * Call Claude with retry logic. Supports both streaming and non-streaming modes.\n * For tool_use calls, returns the parsed tool input. For streaming calls, invokes\n * onToken for each text chunk and returns the full assembled text.\n */\nexport async function callClaude(options: CallClaudeOptions): Promise<string> {\n  const { system, messages, tools, maxTokens = 4096, stream = false, onToken } = options;\n  const anthropic = getClient();\n\n  for (let attempt = 0; attempt <= RETRY_COUNT; attempt++) {\n    try {\n      if (stream) {\n        return await callClaudeStreaming(anthropic, system, messages, maxTokens, onToken);\n      }\n\n      if (tools && tools.length > 0) {\n        return await callClaudeToolUse(anthropic, system, messages, tools, maxTokens);\n      }\n\n      return await callClaudeBasic(anthropic, 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\nasync function callClaudeStreaming(\n  anthropic: Anthropic,\n  system: string,\n  messages: Anthropic.MessageParam[],\n  maxTokens: number,\n  onToken?: (text: string) => void,\n): Promise<string> {\n  const stream = anthropic.messages.stream({\n    model: MODEL,\n    max_tokens: maxTokens,\n    system,\n    messages,\n  });\n\n  let fullText = \"\";\n\n  for await (const event of stream) {\n    if (\n      event.type === \"content_block_delta\" &&\n      event.delta.type === \"text_delta\"\n    ) {\n      fullText += event.delta.text;\n      onToken?.(event.delta.text);\n    }\n  }\n\n  return fullText;\n}\n\nasync function callClaudeToolUse(\n  anthropic: Anthropic,\n  system: string,\n  messages: Anthropic.MessageParam[],\n  tools: Anthropic.Tool[],\n  maxTokens: number,\n): Promise<string> {\n  const response = await anthropic.messages.create({\n    model: MODEL,\n    max_tokens: maxTokens,\n    system,\n    messages,\n    tools,\n  });\n\n  const toolBlock = response.content.find((block) => block.type === \"tool_use\");\n  if (toolBlock && toolBlock.type === \"tool_use\") {\n    return JSON.stringify(toolBlock.input);\n  }\n\n  // Fallback: return text content if no tool use\n  const textBlock = response.content.find((block) => block.type === \"text\");\n  if (textBlock && textBlock.type === \"text\") {\n    return textBlock.text;\n  }\n\n  return \"\";\n}\n\nasync function callClaudeBasic(\n  anthropic: Anthropic,\n  system: string,\n  messages: Anthropic.MessageParam[],\n  maxTokens: number,\n): Promise<string> {\n  const response = await anthropic.messages.create({\n    model: MODEL,\n    max_tokens: maxTokens,\n    system,\n    messages,\n  });\n\n  const textBlock = response.content.find((block) => block.type === \"text\");\n  if (textBlock && textBlock.type === \"text\") {\n    return textBlock.text;\n  }\n\n  return \"\";\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          },\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    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.filter(\n      (c) =>\n        typeof c.concept === \"string\" &&\n        typeof c.summary === \"string\" &&\n        typeof c.is_new === \"boolean\",\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/**\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 = new Set(\n    directChanges\n      .filter((c) => c.status === \"new\" || c.status === \"changed\")\n      .map((c) => c.file),\n  );\n\n  // Deleted files must never be enqueued for recompilation — their source\n  // no longer exists on disk, so compileSource would fail reading it.\n  const deletedFiles = new Set(\n    directChanges\n      .filter((c) => c.status === \"deleted\")\n      .map((c) => c.file),\n  );\n\n  const conceptMap = buildConceptToSourcesMap(state.sources);\n  const affected = new Set<string>();\n\n  for (const changedFile of changedFiles) {\n    const sourceEntry = state.sources[changedFile];\n    if (!sourceEntry) continue;\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 skip = changedFiles.has(contributor)\n          || deletedFiles.has(contributor)\n          || affected.has(contributor);\n        if (!skip) {\n          affected.add(contributor);\n        }\n      }\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 * 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 = new Set(\n    allChanges\n      .filter((c) => c.status === \"new\" || c.status === \"changed\")\n      .map((c) => c.file),\n  );\n  const deletedFiles = new Set(\n    allChanges.filter((c) => c.status === \"deleted\").map((c) => c.file),\n  );\n  const conceptMap = buildConceptToSourcesMap(state.sources);\n\n  // Collect concept slugs from ALL extractions that weren't in the source's\n  // previous concept list. These are \"newly gained\" concepts that\n  // findAffectedSources couldn't have matched pre-extraction.\n  const freshSlugs = new Set<string>();\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)) {\n        freshSlugs.add(slug);\n      }\n    }\n  }\n\n  // Find unchanged sources that own any of those freshly gained slugs.\n  const affected = new Set<string>();\n  for (const slug of freshSlugs) {\n    const owners = conceptMap.get(slug);\n    if (!owners) continue;\n    for (const owner of owners) {\n      if (!compilingFiles.has(owner) && !deletedFiles.has(owner)) {\n        affected.add(owner);\n      }\n    }\n  }\n\n  return Array.from(affected);\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$/, \"\"),\n        title: meta.title,\n        filePath,\n      });\n    }\n  }\n\n  return pages;\n}\n\n/** Check if a position is inside an existing [[wikilink]]. */\nfunction isInsideWikilink(text: string, position: number): boolean {\n  const before = text.lastIndexOf(\"[[\", position);\n  const after = text.indexOf(\"]]\", position);\n  if (before === -1 || after === -1) return false;\n\n  const closeBefore = text.indexOf(\"]]\", before);\n  return closeBefore >= position;\n}\n\n/** Check if a match is at a word boundary. */\nfunction isWordBoundary(text: string, start: number, end: number): boolean {\n  const before = start === 0 || /[\\s,.:;!?()\\[\\]{}/\"']/.test(text[start - 1]);\n  const after = end >= text.length || /[\\s,.:;!?()\\[\\]{}/\"']/.test(text[end]);\n  return before && after;\n}\n\n/**\n * Add [[wikilinks]] to a page's body for any title mentions.\n * Skips already-linked text and non-word-boundary matches.\n */\nfunction addWikilinks(body: string, titles: PageInfo[], selfTitle: string): string {\n  let result = body;\n\n  for (const page of titles) {\n    if (page.title.toLowerCase() === selfTitle.toLowerCase()) continue;\n\n    const escaped = page.title.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n    const regex = new RegExp(escaped, \"gi\");\n    let match;\n\n    // Process matches in reverse to preserve positions\n    const matches: { start: number; end: number }[] = [];\n    while ((match = regex.exec(result)) !== null) {\n      matches.push({ start: match.index, end: match.index + match[0].length });\n    }\n\n    for (const m of matches.reverse()) {\n      if (isInsideWikilink(result, m.start)) continue;\n      if (!isWordBoundary(result, m.start, m.end)) continue;\n\n      result =\n        result.slice(0, m.start) +\n        `[[${page.title}]]` +\n        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 ${total} pages.`));\n}\n\n/**\n * Scan the concepts directory and extract page summaries from frontmatter.\n * @param conceptsPath - Absolute path to wiki/concepts/.\n * @returns Array of page summary objects.\n */\nasync function collectPageSummaries(\n  conceptsPath: string,\n): Promise<PageSummary[]> {\n  let files: string[];\n\n  try {\n    files = await readdir(conceptsPath);\n  } catch {\n    return [];\n  }\n\n  const pages: PageSummary[] = [];\n\n  for (const file of files.filter((f) => f.endsWith(\".md\"))) {\n    const content = await safeReadFile(path.join(conceptsPath, file));\n    const { meta } = parseFrontmatter(content);\n    if (meta.title && typeof meta.title === \"string\" && !meta.orphaned) {\n      pages.push({\n        title: meta.title,\n        slug: file.replace(/\\.md$/, \"\"),\n        summary: typeof meta.summary === \"string\" ? meta.summary : \"\",\n      });\n    }\n  }\n\n  return pages;\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 * 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 Anthropic from \"@anthropic-ai/sdk\";\nimport { callClaude } from \"../utils/llm.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\";\n\n/** Directories to search when loading selected pages, in priority order. */\nconst PAGE_DIRS = [CONCEPTS_DIR, QUERIES_DIR];\n\n/** Anthropic tool schema for page selection. */\nconst PAGE_SELECTION_TOOL: Anthropic.Tool = {\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 */\nasync 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/**\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/**\n * Stream an answer from Claude using the loaded wiki pages as context.\n * @param question - The user's natural language question.\n * @param pagesContent - Combined content of the selected wiki pages.\n * @returns The full answer text after streaming completes.\n */\nasync function streamAnswer(question: string, pagesContent: string): Promise<string> {\n  const systemPrompt =\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  const userMessage = `Question: ${question}\\n\\nRelevant wiki pages:\\n${pagesContent}`;\n\n  const answer = await callClaude({\n    system: systemPrompt,\n    messages: [{ role: \"user\", content: userMessage }],\n    stream: true,\n    onToken: (text: string) => process.stdout.write(text),\n  });\n\n  // Ensure terminal output ends on a new line after streaming\n  process.stdout.write(\"\\n\");\n  return answer;\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<void> {\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\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  // Step 1: Select relevant pages\n  output.header(\"Selecting relevant pages\");\n\n  const indexContent = await safeReadFile(path.join(root, INDEX_FILE));\n  const { pages: rawPages, reasoning } = await selectPages(question, indexContent);\n  const pages = rawPages.map((p) => slugify(p));\n\n  output.status(\"i\", output.dim(`Reasoning: ${reasoning}`));\n  output.status(\"*\", output.info(`Selected ${pages.length} page(s): ${rawPages.join(\", \")}`));\n\n  // Step 2: Load pages and stream the answer\n  output.header(\"Generating answer\");\n\n  const pagesContent = await loadSelectedPages(root, pages);\n\n  if (!pagesContent) {\n    output.status(\"!\", output.error(\"No matching pages found. Try refining your question.\"));\n    return;\n  }\n\n  const answer = await streamAnswer(question, pagesContent);\n\n  // Optional: save the answer as a query page\n  if (options.save) {\n    await saveQueryPage(root, question, answer);\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>(() => 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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "llm-wiki-compiler",
-  "version": "0.1.0",
+  "version": "0.1.1",
   "description": "A knowledge compiler CLI — raw sources in, interlinked wiki out",
   "type": "module",
   "bin": {