@tekmidian/pai 0.35.1 → 0.36.0

package/dist/{vault-indexer-CUF9edbW.mjs.map → vault-indexer-CFvlPUMB.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"vault-indexer-CUF9edbW.mjs","names":[],"sources":["../src/memory/vault/walk.ts","../src/memory/vault/deduplicate.ts","../src/memory/vault/parse-links.ts","../src/memory/vault/name-index.ts","../src/memory/vault/resolve.ts","../src/memory/vault/indexer.ts"],"sourcesContent":["/**\n * Vault directory walker — follows symlinks with cycle detection.\n */\n\nimport { statSync, readdirSync, existsSync } from \"node:fs\";\nimport { join, relative } from \"node:path\";\nimport type { VaultFile } from \"./types.js\";\n\n/** Maximum number of .md files to collect from a vault. */\nconst VAULT_MAX_FILES = 10_000;\n\n/** Maximum recursion depth for vault directory walks. */\nconst VAULT_MAX_DEPTH = 10;\n\n/**\n * Directories to always skip, at any depth, during vault walks.\n * Includes standard build/VCS noise plus Obsidian-specific directories.\n */\nconst VAULT_SKIP_DIRS = new Set([\n  // Version control\n  \".git\",\n  // Dependency directories (any language)\n  \"node_modules\",\n  \"vendor\",\n  \"Pods\",\n  // Build / compile output\n  \"dist\",\n  \"build\",\n  \"out\",\n  \"DerivedData\",\n  \".next\",\n  // Python virtual environments and caches\n  \".venv\",\n  \"venv\",\n  \"__pycache__\",\n  // General caches\n  \".cache\",\n  \".bun\",\n  // Obsidian internals\n  \".obsidian\",\n  \".trash\",\n]);\n\n/**\n * Recursively collect all .md files under a vault root, following symlinks.\n *\n * Symlink-following behaviour:\n *  - Symbolic links to files: followed if the target is a .md file\n *  - Symbolic links to directories: followed with cycle detection via inode\n *\n * Cycle detection is based on the real inode of each visited directory.\n * Using the real stat (not lstat) ensures that symlinked dirs resolve to\n * their actual inode, preventing infinite loops.\n *\n * @param vaultRoot  Absolute path to the vault root directory.\n * @param opts       Optional overrides for maxFiles and maxDepth.\n */\nexport function walkVaultMdFiles(\n  vaultRoot: string,\n  opts?: { maxFiles?: number; maxDepth?: number },\n): VaultFile[] {\n  const maxFiles = opts?.maxFiles ?? VAULT_MAX_FILES;\n  const maxDepth = opts?.maxDepth ?? VAULT_MAX_DEPTH;\n\n  const results: VaultFile[] = [];\n  const visitedDirs = new Set<string>();\n\n  function walk(dir: string, depth: number): void {\n    if (results.length >= maxFiles) return;\n    if (depth > maxDepth) return;\n\n    // Get the real inode of this directory (follows symlinks on the dir itself)\n    let dirStat: ReturnType<typeof statSync>;\n    try {\n      dirStat = statSync(dir);\n    } catch {\n      return; // Unreadable or broken symlink — skip\n    }\n\n    const dirKey = `${dirStat.dev}:${dirStat.ino}`;\n    if (visitedDirs.has(dirKey)) return; // Cycle detected\n    visitedDirs.add(dirKey);\n\n    let entries: import(\"node:fs\").Dirent<string>[];\n    try {\n      entries = readdirSync(dir, { withFileTypes: true, encoding: \"utf8\" });\n    } catch {\n      return; // Unreadable directory — skip\n    }\n\n    for (const entry of entries) {\n      if (results.length >= maxFiles) break;\n      if (VAULT_SKIP_DIRS.has(entry.name)) continue;\n\n      const full = join(dir, entry.name);\n\n      if (entry.isSymbolicLink()) {\n        // Follow the symlink — resolve to real target\n        let targetStat: ReturnType<typeof statSync>;\n        try {\n          targetStat = statSync(full); // statSync follows symlinks\n        } catch {\n          continue; // Broken symlink — skip\n        }\n\n        if (targetStat.isDirectory()) {\n          if (!VAULT_SKIP_DIRS.has(entry.name)) {\n            walk(full, depth + 1);\n          }\n        } else if (targetStat.isFile() && entry.name.endsWith(\".md\")) {\n          results.push({\n            absPath: full,\n            vaultRelPath: relative(vaultRoot, full),\n            inode: targetStat.ino,\n            device: targetStat.dev,\n          });\n        }\n      } else if (entry.isDirectory()) {\n        walk(full, depth + 1);\n      } else if (entry.isFile() && entry.name.endsWith(\".md\")) {\n        let fileStat: ReturnType<typeof statSync>;\n        try {\n          fileStat = statSync(full);\n        } catch {\n          continue;\n        }\n        results.push({\n          absPath: full,\n          vaultRelPath: relative(vaultRoot, full),\n          inode: fileStat.ino,\n          device: fileStat.dev,\n        });\n      }\n    }\n  }\n\n  if (existsSync(vaultRoot)) {\n    walk(vaultRoot, 0);\n  }\n\n  return results;\n}\n","/**\n * Inode-based deduplication for vault files.\n */\n\nimport type { VaultFile, InodeGroup } from \"./types.js\";\n\n/**\n * Group vault files by inode identity (device + inode).\n *\n * Within each group, the canonical file is chosen as the one with the\n * fewest path separators (shallowest), breaking ties by shortest string.\n * All other group members become aliases.\n */\nexport function deduplicateByInode(files: VaultFile[]): InodeGroup[] {\n  const groups = new Map<string, VaultFile[]>();\n\n  for (const file of files) {\n    const key = `${file.device}:${file.inode}`;\n    const existing = groups.get(key);\n    if (existing) {\n      existing.push(file);\n    } else {\n      groups.set(key, [file]);\n    }\n  }\n\n  const result: InodeGroup[] = [];\n\n  for (const group of groups.values()) {\n    if (group.length === 0) continue;\n\n    // Sort: fewest path separators first, then shortest string\n    const sorted = [...group].sort((a, b) => {\n      const aDepth = (a.vaultRelPath.match(/\\//g) ?? []).length;\n      const bDepth = (b.vaultRelPath.match(/\\//g) ?? []).length;\n      if (aDepth !== bDepth) return aDepth - bDepth;\n      return a.vaultRelPath.length - b.vaultRelPath.length;\n    });\n\n    const [canonical, ...aliases] = sorted as [VaultFile, ...VaultFile[]];\n    result.push({ canonical, aliases });\n  }\n\n  return result;\n}\n","/**\n * Markdown link parser for vault files.\n *\n * Handles wikilinks ([[target]]), markdown links ([text](path)),\n * embeds (![[target]]), and frontmatter wikilinks.\n */\n\nimport type { ParsedLink } from \"./types.js\";\n\n/**\n * Parse all links from markdown content.\n *\n * Handles:\n *  - Standard wikilinks: [[Target Note]]\n *  - Aliased wikilinks: [[Target Note|Display Text]]\n *  - Heading anchors: [[Target Note#Heading]] (stripped for resolution)\n *  - Embeds: ![[Target Note]]\n *  - Frontmatter wikilinks (YAML between --- delimiters)\n *  - Markdown links: [text](path/to/note.md)\n *  - Markdown embeds: ![alt](image.png)\n *\n * External URLs (http://, https://, mailto:, etc.) are excluded — only\n * relative paths are treated as vault links.\n *\n * @param content  Raw markdown file content.\n * @returns        Array of parsed links in document order.\n */\nexport function parseLinks(content: string): ParsedLink[] {\n  const links: ParsedLink[] = [];\n  const lines = content.split(\"\\n\");\n\n  // Determine frontmatter range (YAML between opening and closing ---)\n  let frontmatterEnd = 0;\n  if (content.startsWith(\"---\")) {\n    const closingIdx = content.indexOf(\"\\n---\", 3);\n    if (closingIdx !== -1) {\n      frontmatterEnd = content.slice(0, closingIdx + 4).split(\"\\n\").length - 1;\n    }\n  }\n\n  // Regex for [[wikilinks]] and ![[embeds]]\n  const wikilinkRe = /(!?)\\[\\[([^\\]]+?)\\]\\]/g;\n\n  // Regex for markdown links [text](target) and embeds ![alt](target)\n  const mdLinkRe = /(!)?\\[([^\\]]*)\\]\\(([^)]+)\\)/g;\n\n  for (let lineIdx = 0; lineIdx < lines.length; lineIdx++) {\n    const line = lines[lineIdx]!;\n    const lineNumber = lineIdx + 1; // 1-indexed\n    const isFrontmatter = lineIdx < frontmatterEnd;\n\n    // --- Wikilinks ---\n    wikilinkRe.lastIndex = 0;\n    let match: RegExpExecArray | null;\n    while ((match = wikilinkRe.exec(line)) !== null) {\n      const isEmbed = match[1] === \"!\";\n      const inner = match[2]!;\n\n      // Split on first | for alias\n      const pipeIdx = inner.indexOf(\"|\");\n      const beforePipe = pipeIdx === -1 ? inner : inner.slice(0, pipeIdx);\n      const alias = pipeIdx === -1 ? null : inner.slice(pipeIdx + 1);\n\n      // Strip heading anchor (everything after #)\n      const hashIdx = beforePipe.indexOf(\"#\");\n      const raw = hashIdx === -1 ? beforePipe.trim() : beforePipe.slice(0, hashIdx).trim();\n\n      if (!raw) continue; // Skip links with empty targets (e.g. [[#Heading]])\n\n      links.push({\n        raw,\n        alias: alias?.trim() ?? null,\n        lineNumber,\n        isEmbed: isEmbed && !isFrontmatter,\n        isMdLink: false,\n      });\n    }\n\n    // --- Markdown links --- (skip inside frontmatter)\n    if (!isFrontmatter) {\n      mdLinkRe.lastIndex = 0;\n      while ((match = mdLinkRe.exec(line)) !== null) {\n        const isEmbed = match[1] === \"!\";\n        const displayText = match[2]!;\n        let target = match[3]!.trim();\n\n        // Skip external URLs\n        if (/^[a-z][a-z0-9+.-]*:/i.test(target)) continue;\n\n        // Skip pure anchor links (#heading)\n        if (target.startsWith(\"#\")) continue;\n\n        // Strip heading anchor from target\n        const hashIdx = target.indexOf(\"#\");\n        if (hashIdx !== -1) target = target.slice(0, hashIdx);\n\n        // URL-decode (Obsidian encodes spaces as %20 in md links)\n        try {\n          target = decodeURIComponent(target);\n        } catch {\n          // Malformed encoding — use as-is\n        }\n\n        // Strip .md extension for resolution (resolveWikilink adds it back)\n        const raw = target.replace(/\\.md$/i, \"\").trim();\n        if (!raw) continue;\n\n        links.push({\n          raw,\n          alias: displayText || null,\n          lineNumber,\n          isEmbed,\n          isMdLink: true,\n        });\n      }\n    }\n  }\n\n  return links;\n}\n\n/** @deprecated Use {@link parseLinks} instead. */\nexport const parseWikilinks = parseLinks;\n","/**\n * Name index builder for Obsidian wikilink resolution.\n */\n\nimport { basename } from \"node:path\";\nimport type { VaultFile } from \"./types.js\";\n\n/**\n * Build a name lookup index for Obsidian wikilink resolution.\n *\n * Maps lowercase filename (without .md extension) to all vault-relative paths\n * that share that name. Includes both canonical paths and alias paths so that\n * wikilinks resolve regardless of which path the file is accessed through.\n */\nexport function buildNameIndex(files: VaultFile[]): Map<string, string[]> {\n  const index = new Map<string, string[]>();\n\n  for (const file of files) {\n    const name = basename(file.vaultRelPath, \".md\").toLowerCase();\n    const existing = index.get(name);\n    if (existing) {\n      existing.push(file.vaultRelPath);\n    } else {\n      index.set(name, [file.vaultRelPath]);\n    }\n  }\n\n  return index;\n}\n","/**\n * Wikilink resolver using Obsidian's shortest-match algorithm.\n */\n\nimport { normalize, basename, dirname } from \"node:path\";\n\n/**\n * Resolve a wikilink target to a vault-relative path using Obsidian's rules.\n *\n * Resolution algorithm:\n *  1. If raw contains \"/\", attempt exact path match (with and without .md).\n *  2. Normalize: lowercase the raw target, strip .md extension.\n *  3. Look up in the name index (all files with that basename).\n *  4. If exactly one match, return it.\n *  5. If multiple matches, pick the one closest to the source file\n *     (longest common directory prefix, then shortest overall path).\n *  6. If no matches, return null (dead link).\n *\n * @param raw         The raw link target (heading-stripped, pipe-stripped).\n * @param nameIndex   Map from lowercase basename-without-ext to vault paths.\n * @param sourcePath  Vault-relative path of the file containing the link.\n * @returns           Vault-relative path of the resolved target, or null.\n */\nexport function resolveWikilink(\n  raw: string,\n  nameIndex: Map<string, string[]>,\n  sourcePath: string,\n): string | null {\n  if (!raw) return null;\n\n  // Case 1: path contains \"/\" — try exact match with and without .md\n  if (raw.includes(\"/\")) {\n    const normalized = normalize(raw);\n    const normalizedMd = normalized.endsWith(\".md\") ? normalized : normalized + \".md\";\n\n    // Check if any indexed path matches (case-insensitive for macOS compatibility)\n    for (const [, paths] of nameIndex) {\n      for (const p of paths) {\n        if (p === normalizedMd || p === normalized) return p;\n        if (p.toLowerCase() === normalizedMd.toLowerCase()) return p;\n      }\n    }\n    // Fall through to name lookup in case the path prefix was wrong\n  }\n\n  // Normalize the raw target for name lookup.\n  // Use the basename only — Obsidian resolves by filename, not full path.\n  const rawBase = basename(raw)\n    .replace(/\\.md$/i, \"\")\n    .toLowerCase()\n    .trim();\n\n  if (!rawBase) return null;\n\n  const candidates = nameIndex.get(rawBase);\n\n  if (!candidates || candidates.length === 0) {\n    return null; // Dead link\n  }\n\n  if (candidates.length === 1) {\n    return candidates[0]!;\n  }\n\n  // Multiple matches — pick the one closest to the source file\n  const sourceDir = dirname(sourcePath);\n\n  let bestPath: string | null = null;\n  let bestPrefixLen = -1;\n  let bestPathLen = Infinity;\n\n  for (const candidate of candidates) {\n    const candidateDir = dirname(candidate);\n    const prefixLen = commonPrefixLength(sourceDir, candidateDir);\n    const pathLen = candidate.length;\n\n    if (\n      prefixLen > bestPrefixLen ||\n      (prefixLen === bestPrefixLen && pathLen < bestPathLen)\n    ) {\n      bestPrefixLen = prefixLen;\n      bestPathLen = pathLen;\n      bestPath = candidate;\n    }\n  }\n\n  return bestPath;\n}\n\n/**\n * Compute the length of the common prefix between two directory paths,\n * measured in path segments (not raw characters).\n *\n * Example: \"a/b/c\" and \"a/b/d\" → 2 (common: \"a\", \"b\")\n */\nfunction commonPrefixLength(a: string, b: string): number {\n  if (a === \".\" && b === \".\") return 0;\n  const aParts = a === \".\" ? [] : a.split(\"/\");\n  const bParts = b === \".\" ? [] : b.split(\"/\");\n  let count = 0;\n  const len = Math.min(aParts.length, bParts.length);\n  for (let i = 0; i < len; i++) {\n    if (aParts[i] === bParts[i]) {\n      count++;\n    } else {\n      break;\n    }\n  }\n  return count;\n}\n","/**\n * Main vault indexing orchestrator.\n *\n * Indexes an entire Obsidian vault (or any markdown knowledge base), following\n * symlinks, deduplicating files by inode, parsing wikilinks, and computing\n * per-file health metrics (orphan detection, dead links).\n *\n * Key differences from the project indexer (indexer/sync.ts):\n *  - Follows symbolic links (project indexer skips them)\n *  - Deduplicates files with the same inode (same content reachable via multiple paths)\n *  - Parses [[wikilinks]] and builds a directed link graph\n *  - Resolves wikilinks using Obsidian's shortest-match algorithm\n *  - Computes health metrics per file: inbound/outbound link counts, dead links, orphans\n */\n\nimport { readFileSync } from \"node:fs\";\nimport { basename } from \"node:path\";\nimport type {\n  StorageBackend,\n  VaultFileRow,\n  VaultAliasRow,\n  VaultLinkRow,\n  VaultHealthRow,\n  VaultNameEntry,\n  ChunkRow,\n} from \"../../storage/interface.js\";\nimport { chunkMarkdown } from \"../chunker.js\";\nimport { sha256File, chunkId, yieldToEventLoop } from \"../indexer/helpers.js\";\nimport { walkVaultMdFiles } from \"./walk.js\";\nimport { deduplicateByInode } from \"./deduplicate.js\";\nimport { parseLinks } from \"./parse-links.js\";\nimport { buildNameIndex } from \"./name-index.js\";\nimport { resolveWikilink } from \"./resolve.js\";\nimport type { VaultIndexResult } from \"./types.js\";\n\n/** Number of files to process before yielding to the event loop. */\nconst VAULT_YIELD_EVERY = 1;\n\n/**\n * Index an entire Obsidian vault (or markdown knowledge base) using the\n * async StorageBackend interface.\n *\n * Steps:\n *  1. Walk vault root, following symlinks.\n *  2. Deduplicate by inode — each unique file is indexed once.\n *  3. Build a name index for wikilink resolution.\n *  4. For each canonical file:\n *     a. SHA-256 hash for change detection — skip unchanged files.\n *     b. Read content, chunk with chunkMarkdown().\n *     c. Insert chunks into backend (memory_chunks and memory_fts).\n *     d. Upsert vault_files row.\n *  5. Record aliases in vault_aliases.\n *  6. Rebuild vault_name_index table.\n *  7. Rebuild vault_links:\n *     a. Parse [[wikilinks]] from each canonical file.\n *     b. Resolve each link with resolveWikilink().\n *     c. Insert into vault_links.\n *  8. Compute and upsert health metrics (vault_health).\n *  9. Return statistics.\n *\n * @param backend         StorageBackend to write to.\n * @param vaultProjectId  Registry project ID for the vault \"project\".\n * @param vaultRoot       Absolute path to the vault root directory.\n */\nexport async function indexVault(\n  backend: StorageBackend,\n  vaultProjectId: number,\n  vaultRoot: string,\n): Promise<VaultIndexResult> {\n  const startTime = Date.now();\n\n  const result: VaultIndexResult = {\n    filesIndexed: 0,\n    chunksCreated: 0,\n    filesSkipped: 0,\n    aliasesRecorded: 0,\n    linksExtracted: 0,\n    deadLinksFound: 0,\n    orphansFound: 0,\n    elapsed: 0,\n  };\n\n  // Step 1: Walk vault, collecting all .md files (follows symlinks)\n  const allFiles = walkVaultMdFiles(vaultRoot);\n\n  // Step 2: Deduplicate by inode\n  const inodeGroups = deduplicateByInode(allFiles);\n\n  // Step 3: Build name index (from all files including aliases, for resolution)\n  const nameIndex = buildNameIndex(allFiles);\n\n  // Step 4: Index each canonical file\n  await yieldToEventLoop();\n  let filesSinceYield = 0;\n\n  for (const group of inodeGroups) {\n    if (filesSinceYield >= VAULT_YIELD_EVERY) {\n      await yieldToEventLoop();\n      filesSinceYield = 0;\n    }\n    filesSinceYield++;\n\n    const { canonical } = group;\n\n    let content: string;\n    try {\n      content = readFileSync(canonical.absPath, \"utf8\");\n    } catch {\n      result.filesSkipped++;\n      continue;\n    }\n\n    const hash = sha256File(content);\n\n    // Change detection: skip if hash is unchanged\n    const existing = await backend.getVaultFile(canonical.vaultRelPath);\n    if (existing?.hash === hash) {\n      result.filesSkipped++;\n      continue;\n    }\n\n    // Delete old chunks for this vault path\n    await backend.deleteChunksForFile(vaultProjectId, canonical.vaultRelPath);\n\n    // Chunk the content\n    const chunks = chunkMarkdown(content);\n    const updatedAt = Date.now();\n\n    // Extract title from first H1 heading or filename\n    const titleMatch = /^#\\s+(.+)$/m.exec(content);\n    const title = titleMatch\n      ? titleMatch[1]!.trim()\n      : basename(canonical.vaultRelPath, \".md\");\n\n    // Build chunk rows\n    const chunkRows: ChunkRow[] = [];\n    for (let i = 0; i < chunks.length; i++) {\n      const chunk = chunks[i]!;\n      const id = chunkId(\n        vaultProjectId,\n        canonical.vaultRelPath,\n        i,\n        chunk.startLine,\n        chunk.endLine,\n      );\n      chunkRows.push({\n        id,\n        projectId: vaultProjectId,\n        source: \"vault\",\n        tier: \"topic\",\n        path: canonical.vaultRelPath,\n        startLine: chunk.startLine,\n        endLine: chunk.endLine,\n        hash: chunk.hash,\n        text: chunk.text,\n        updatedAt,\n      });\n    }\n\n    if (chunkRows.length > 0) {\n      await backend.insertChunks(chunkRows);\n    }\n\n    // Upsert vault file record\n    const vaultFileRow: VaultFileRow = {\n      vaultPath: canonical.vaultRelPath,\n      inode: canonical.inode,\n      device: canonical.device,\n      hash,\n      title,\n      indexedAt: updatedAt,\n    };\n    await backend.upsertVaultFile(vaultFileRow);\n\n    result.filesIndexed++;\n    result.chunksCreated += chunks.length;\n  }\n\n  // Step 5: Record aliases in vault_aliases\n  await yieldToEventLoop();\n\n  const allAliases: VaultAliasRow[] = [];\n  for (const group of inodeGroups) {\n    for (const alias of group.aliases) {\n      allAliases.push({\n        vaultPath: alias.vaultRelPath,\n        canonicalPath: group.canonical.vaultRelPath,\n        inode: alias.inode,\n        device: alias.device,\n      });\n      result.aliasesRecorded++;\n    }\n  }\n\n  const canonicalPaths = new Set(inodeGroups.map((g) => g.canonical.vaultRelPath));\n  for (const canonPath of canonicalPaths) {\n    await backend.deleteVaultAliases(canonPath);\n  }\n  if (allAliases.length > 0) {\n    await backend.upsertVaultAliases(allAliases);\n  }\n\n  // Step 6: Rebuild vault_name_index\n  await yieldToEventLoop();\n\n  const nameEntries: VaultNameEntry[] = [];\n  for (const [name, paths] of nameIndex) {\n    for (const path of paths) {\n      nameEntries.push({ name, vaultPath: path });\n    }\n  }\n  await backend.replaceNameIndex(nameEntries);\n\n  // Step 7: Rebuild vault_links\n  await yieldToEventLoop();\n\n  const linkRows: VaultLinkRow[] = [];\n  const allSourcePaths: string[] = [];\n\n  let linkParseYield = 0;\n  for (const group of inodeGroups) {\n    if (linkParseYield++ % VAULT_YIELD_EVERY === 0) {\n      await yieldToEventLoop();\n    }\n\n    const { canonical } = group;\n    allSourcePaths.push(canonical.vaultRelPath);\n\n    let content: string;\n    try {\n      content = readFileSync(canonical.absPath, \"utf8\");\n    } catch {\n      continue;\n    }\n\n    const parsedLinks = parseLinks(content);\n    for (const link of parsedLinks) {\n      const target = resolveWikilink(link.raw, nameIndex, canonical.vaultRelPath);\n      let linkType: string;\n      if (link.isMdLink) {\n        linkType = link.isEmbed ? \"md-embed\" : \"md-link\";\n      } else {\n        linkType = link.isEmbed ? \"embed\" : \"wikilink\";\n      }\n      linkRows.push({\n        sourcePath: canonical.vaultRelPath,\n        targetRaw: link.raw,\n        targetPath: target,\n        linkType,\n        lineNumber: link.lineNumber,\n        confidence: \"EXTRACTED\",\n      });\n    }\n  }\n\n  // Replace all links for all sources in batches of 500\n  const LINK_BATCH_SIZE = 500;\n  for (let i = 0; i < allSourcePaths.length; i += LINK_BATCH_SIZE) {\n    const batchSources = allSourcePaths.slice(i, i + LINK_BATCH_SIZE);\n    const batchLinks = linkRows.filter((r) => batchSources.includes(r.sourcePath));\n    await backend.replaceLinksForSources(batchSources, batchLinks);\n    await yieldToEventLoop();\n  }\n\n  result.linksExtracted = linkRows.length;\n  result.deadLinksFound = linkRows.filter((r) => r.targetPath === null).length;\n\n  // Step 8: Compute and upsert vault_health metrics\n  await yieldToEventLoop();\n\n  const outboundMap = new Map<string, number>();\n  const deadMap = new Map<string, number>();\n  const inboundMap = new Map<string, number>();\n\n  for (const row of linkRows) {\n    outboundMap.set(row.sourcePath, (outboundMap.get(row.sourcePath) ?? 0) + 1);\n    if (row.targetPath === null) {\n      deadMap.set(row.sourcePath, (deadMap.get(row.sourcePath) ?? 0) + 1);\n    } else {\n      inboundMap.set(row.targetPath, (inboundMap.get(row.targetPath) ?? 0) + 1);\n    }\n  }\n\n  const computedAt = Date.now();\n  let orphanCount = 0;\n\n  const HEALTH_BATCH_SIZE = 500;\n  for (let i = 0; i < inodeGroups.length; i += HEALTH_BATCH_SIZE) {\n    const batch = inodeGroups.slice(i, i + HEALTH_BATCH_SIZE);\n    const healthRows: VaultHealthRow[] = batch.map((group) => {\n      const path = group.canonical.vaultRelPath;\n      const inbound = inboundMap.get(path) ?? 0;\n      const outbound = outboundMap.get(path) ?? 0;\n      const dead = deadMap.get(path) ?? 0;\n      const isOrphan = inbound === 0;\n      if (isOrphan) orphanCount++;\n      return {\n        vaultPath: path,\n        inboundCount: inbound,\n        outboundCount: outbound,\n        deadLinkCount: dead,\n        isOrphan,\n        computedAt,\n      };\n    });\n    await backend.upsertVaultHealth(healthRows);\n    await yieldToEventLoop();\n  }\n\n  result.orphansFound = orphanCount;\n  result.elapsed = Date.now() - startTime;\n\n  return 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+{"version":3,"file":"vault-indexer-CFvlPUMB.mjs","names":[],"sources":["../src/memory/vault/walk.ts","../src/memory/vault/deduplicate.ts","../src/memory/vault/parse-links.ts","../src/memory/vault/name-index.ts","../src/memory/vault/resolve.ts","../src/memory/vault/indexer.ts"],"sourcesContent":["/**\n * Vault directory walker — follows symlinks with cycle detection.\n */\n\nimport { statSync, readdirSync, existsSync } from \"node:fs\";\nimport { join, relative } from \"node:path\";\nimport type { VaultFile } from \"./types.js\";\n\n/** Maximum number of .md files to collect from a vault. */\nconst VAULT_MAX_FILES = 10_000;\n\n/** Maximum recursion depth for vault directory walks. */\nconst VAULT_MAX_DEPTH = 10;\n\n/**\n * Directories to always skip, at any depth, during vault walks.\n * Includes standard build/VCS noise plus Obsidian-specific directories.\n */\nconst VAULT_SKIP_DIRS = new Set([\n  // Version control\n  \".git\",\n  // Dependency directories (any language)\n  \"node_modules\",\n  \"vendor\",\n  \"Pods\",\n  // Build / compile output\n  \"dist\",\n  \"build\",\n  \"out\",\n  \"DerivedData\",\n  \".next\",\n  // Python virtual environments and caches\n  \".venv\",\n  \"venv\",\n  \"__pycache__\",\n  // General caches\n  \".cache\",\n  \".bun\",\n  // Obsidian internals\n  \".obsidian\",\n  \".trash\",\n]);\n\n/**\n * Recursively collect all .md files under a vault root, following symlinks.\n *\n * Symlink-following behaviour:\n *  - Symbolic links to files: followed if the target is a .md file\n *  - Symbolic links to directories: followed with cycle detection via inode\n *\n * Cycle detection is based on the real inode of each visited directory.\n * Using the real stat (not lstat) ensures that symlinked dirs resolve to\n * their actual inode, preventing infinite loops.\n *\n * @param vaultRoot  Absolute path to the vault root directory.\n * @param opts       Optional overrides for maxFiles and maxDepth.\n */\nexport function walkVaultMdFiles(\n  vaultRoot: string,\n  opts?: { maxFiles?: number; maxDepth?: number },\n): VaultFile[] {\n  const maxFiles = opts?.maxFiles ?? VAULT_MAX_FILES;\n  const maxDepth = opts?.maxDepth ?? VAULT_MAX_DEPTH;\n\n  const results: VaultFile[] = [];\n  const visitedDirs = new Set<string>();\n\n  function walk(dir: string, depth: number): void {\n    if (results.length >= maxFiles) return;\n    if (depth > maxDepth) return;\n\n    // Get the real inode of this directory (follows symlinks on the dir itself)\n    let dirStat: ReturnType<typeof statSync>;\n    try {\n      dirStat = statSync(dir);\n    } catch {\n      return; // Unreadable or broken symlink — skip\n    }\n\n    const dirKey = `${dirStat.dev}:${dirStat.ino}`;\n    if (visitedDirs.has(dirKey)) return; // Cycle detected\n    visitedDirs.add(dirKey);\n\n    let entries: import(\"node:fs\").Dirent<string>[];\n    try {\n      entries = readdirSync(dir, { withFileTypes: true, encoding: \"utf8\" });\n    } catch {\n      return; // Unreadable directory — skip\n    }\n\n    for (const entry of entries) {\n      if (results.length >= maxFiles) break;\n      if (VAULT_SKIP_DIRS.has(entry.name)) continue;\n\n      const full = join(dir, entry.name);\n\n      if (entry.isSymbolicLink()) {\n        // Follow the symlink — resolve to real target\n        let targetStat: ReturnType<typeof statSync>;\n        try {\n          targetStat = statSync(full); // statSync follows symlinks\n        } catch {\n          continue; // Broken symlink — skip\n        }\n\n        if (targetStat.isDirectory()) {\n          if (!VAULT_SKIP_DIRS.has(entry.name)) {\n            walk(full, depth + 1);\n          }\n        } else if (targetStat.isFile() && entry.name.endsWith(\".md\")) {\n          results.push({\n            absPath: full,\n            vaultRelPath: relative(vaultRoot, full),\n            inode: targetStat.ino,\n            device: targetStat.dev,\n          });\n        }\n      } else if (entry.isDirectory()) {\n        walk(full, depth + 1);\n      } else if (entry.isFile() && entry.name.endsWith(\".md\")) {\n        let fileStat: ReturnType<typeof statSync>;\n        try {\n          fileStat = statSync(full);\n        } catch {\n          continue;\n        }\n        results.push({\n          absPath: full,\n          vaultRelPath: relative(vaultRoot, full),\n          inode: fileStat.ino,\n          device: fileStat.dev,\n        });\n      }\n    }\n  }\n\n  if (existsSync(vaultRoot)) {\n    walk(vaultRoot, 0);\n  }\n\n  return results;\n}\n","/**\n * Inode-based deduplication for vault files.\n */\n\nimport type { VaultFile, InodeGroup } from \"./types.js\";\n\n/**\n * Group vault files by inode identity (device + inode).\n *\n * Within each group, the canonical file is chosen as the one with the\n * fewest path separators (shallowest), breaking ties by shortest string.\n * All other group members become aliases.\n */\nexport function deduplicateByInode(files: VaultFile[]): InodeGroup[] {\n  const groups = new Map<string, VaultFile[]>();\n\n  for (const file of files) {\n    const key = `${file.device}:${file.inode}`;\n    const existing = groups.get(key);\n    if (existing) {\n      existing.push(file);\n    } else {\n      groups.set(key, [file]);\n    }\n  }\n\n  const result: InodeGroup[] = [];\n\n  for (const group of groups.values()) {\n    if (group.length === 0) continue;\n\n    // Sort: fewest path separators first, then shortest string\n    const sorted = [...group].sort((a, b) => {\n      const aDepth = (a.vaultRelPath.match(/\\//g) ?? []).length;\n      const bDepth = (b.vaultRelPath.match(/\\//g) ?? []).length;\n      if (aDepth !== bDepth) return aDepth - bDepth;\n      return a.vaultRelPath.length - b.vaultRelPath.length;\n    });\n\n    const [canonical, ...aliases] = sorted as [VaultFile, ...VaultFile[]];\n    result.push({ canonical, aliases });\n  }\n\n  return result;\n}\n","/**\n * Markdown link parser for vault files.\n *\n * Handles wikilinks ([[target]]), markdown links ([text](path)),\n * embeds (![[target]]), and frontmatter wikilinks.\n */\n\nimport type { ParsedLink } from \"./types.js\";\n\n/**\n * Parse all links from markdown content.\n *\n * Handles:\n *  - Standard wikilinks: [[Target Note]]\n *  - Aliased wikilinks: [[Target Note|Display Text]]\n *  - Heading anchors: [[Target Note#Heading]] (stripped for resolution)\n *  - Embeds: ![[Target Note]]\n *  - Frontmatter wikilinks (YAML between --- delimiters)\n *  - Markdown links: [text](path/to/note.md)\n *  - Markdown embeds: ![alt](image.png)\n *\n * External URLs (http://, https://, mailto:, etc.) are excluded — only\n * relative paths are treated as vault links.\n *\n * @param content  Raw markdown file content.\n * @returns        Array of parsed links in document order.\n */\nexport function parseLinks(content: string): ParsedLink[] {\n  const links: ParsedLink[] = [];\n  const lines = content.split(\"\\n\");\n\n  // Determine frontmatter range (YAML between opening and closing ---)\n  let frontmatterEnd = 0;\n  if (content.startsWith(\"---\")) {\n    const closingIdx = content.indexOf(\"\\n---\", 3);\n    if (closingIdx !== -1) {\n      frontmatterEnd = content.slice(0, closingIdx + 4).split(\"\\n\").length - 1;\n    }\n  }\n\n  // Regex for [[wikilinks]] and ![[embeds]]\n  const wikilinkRe = /(!?)\\[\\[([^\\]]+?)\\]\\]/g;\n\n  // Regex for markdown links [text](target) and embeds ![alt](target)\n  const mdLinkRe = /(!)?\\[([^\\]]*)\\]\\(([^)]+)\\)/g;\n\n  for (let lineIdx = 0; lineIdx < lines.length; lineIdx++) {\n    const line = lines[lineIdx]!;\n    const lineNumber = lineIdx + 1; // 1-indexed\n    const isFrontmatter = lineIdx < frontmatterEnd;\n\n    // --- Wikilinks ---\n    wikilinkRe.lastIndex = 0;\n    let match: RegExpExecArray | null;\n    while ((match = wikilinkRe.exec(line)) !== null) {\n      const isEmbed = match[1] === \"!\";\n      const inner = match[2]!;\n\n      // Split on first | for alias\n      const pipeIdx = inner.indexOf(\"|\");\n      const beforePipe = pipeIdx === -1 ? inner : inner.slice(0, pipeIdx);\n      const alias = pipeIdx === -1 ? null : inner.slice(pipeIdx + 1);\n\n      // Strip heading anchor (everything after #)\n      const hashIdx = beforePipe.indexOf(\"#\");\n      const raw = hashIdx === -1 ? beforePipe.trim() : beforePipe.slice(0, hashIdx).trim();\n\n      if (!raw) continue; // Skip links with empty targets (e.g. [[#Heading]])\n\n      links.push({\n        raw,\n        alias: alias?.trim() ?? null,\n        lineNumber,\n        isEmbed: isEmbed && !isFrontmatter,\n        isMdLink: false,\n      });\n    }\n\n    // --- Markdown links --- (skip inside frontmatter)\n    if (!isFrontmatter) {\n      mdLinkRe.lastIndex = 0;\n      while ((match = mdLinkRe.exec(line)) !== null) {\n        const isEmbed = match[1] === \"!\";\n        const displayText = match[2]!;\n        let target = match[3]!.trim();\n\n        // Skip external URLs\n        if (/^[a-z][a-z0-9+.-]*:/i.test(target)) continue;\n\n        // Skip pure anchor links (#heading)\n        if (target.startsWith(\"#\")) continue;\n\n        // Strip heading anchor from target\n        const hashIdx = target.indexOf(\"#\");\n        if (hashIdx !== -1) target = target.slice(0, hashIdx);\n\n        // URL-decode (Obsidian encodes spaces as %20 in md links)\n        try {\n          target = decodeURIComponent(target);\n        } catch {\n          // Malformed encoding — use as-is\n        }\n\n        // Strip .md extension for resolution (resolveWikilink adds it back)\n        const raw = target.replace(/\\.md$/i, \"\").trim();\n        if (!raw) continue;\n\n        links.push({\n          raw,\n          alias: displayText || null,\n          lineNumber,\n          isEmbed,\n          isMdLink: true,\n        });\n      }\n    }\n  }\n\n  return links;\n}\n\n/** @deprecated Use {@link parseLinks} instead. */\nexport const parseWikilinks = parseLinks;\n","/**\n * Name index builder for Obsidian wikilink resolution.\n */\n\nimport { basename } from \"node:path\";\nimport type { VaultFile } from \"./types.js\";\n\n/**\n * Build a name lookup index for Obsidian wikilink resolution.\n *\n * Maps lowercase filename (without .md extension) to all vault-relative paths\n * that share that name. Includes both canonical paths and alias paths so that\n * wikilinks resolve regardless of which path the file is accessed through.\n */\nexport function buildNameIndex(files: VaultFile[]): Map<string, string[]> {\n  const index = new Map<string, string[]>();\n\n  for (const file of files) {\n    const name = basename(file.vaultRelPath, \".md\").toLowerCase();\n    const existing = index.get(name);\n    if (existing) {\n      existing.push(file.vaultRelPath);\n    } else {\n      index.set(name, [file.vaultRelPath]);\n    }\n  }\n\n  return index;\n}\n","/**\n * Wikilink resolver using Obsidian's shortest-match algorithm.\n */\n\nimport { normalize, basename, dirname } from \"node:path\";\n\n/**\n * Resolve a wikilink target to a vault-relative path using Obsidian's rules.\n *\n * Resolution algorithm:\n *  1. If raw contains \"/\", attempt exact path match (with and without .md).\n *  2. Normalize: lowercase the raw target, strip .md extension.\n *  3. Look up in the name index (all files with that basename).\n *  4. If exactly one match, return it.\n *  5. If multiple matches, pick the one closest to the source file\n *     (longest common directory prefix, then shortest overall path).\n *  6. If no matches, return null (dead link).\n *\n * @param raw         The raw link target (heading-stripped, pipe-stripped).\n * @param nameIndex   Map from lowercase basename-without-ext to vault paths.\n * @param sourcePath  Vault-relative path of the file containing the link.\n * @returns           Vault-relative path of the resolved target, or null.\n */\nexport function resolveWikilink(\n  raw: string,\n  nameIndex: Map<string, string[]>,\n  sourcePath: string,\n): string | null {\n  if (!raw) return null;\n\n  // Case 1: path contains \"/\" — try exact match with and without .md\n  if (raw.includes(\"/\")) {\n    const normalized = normalize(raw);\n    const normalizedMd = normalized.endsWith(\".md\") ? normalized : normalized + \".md\";\n\n    // Check if any indexed path matches (case-insensitive for macOS compatibility)\n    for (const [, paths] of nameIndex) {\n      for (const p of paths) {\n        if (p === normalizedMd || p === normalized) return p;\n        if (p.toLowerCase() === normalizedMd.toLowerCase()) return p;\n      }\n    }\n    // Fall through to name lookup in case the path prefix was wrong\n  }\n\n  // Normalize the raw target for name lookup.\n  // Use the basename only — Obsidian resolves by filename, not full path.\n  const rawBase = basename(raw)\n    .replace(/\\.md$/i, \"\")\n    .toLowerCase()\n    .trim();\n\n  if (!rawBase) return null;\n\n  const candidates = nameIndex.get(rawBase);\n\n  if (!candidates || candidates.length === 0) {\n    return null; // Dead link\n  }\n\n  if (candidates.length === 1) {\n    return candidates[0]!;\n  }\n\n  // Multiple matches — pick the one closest to the source file\n  const sourceDir = dirname(sourcePath);\n\n  let bestPath: string | null = null;\n  let bestPrefixLen = -1;\n  let bestPathLen = Infinity;\n\n  for (const candidate of candidates) {\n    const candidateDir = dirname(candidate);\n    const prefixLen = commonPrefixLength(sourceDir, candidateDir);\n    const pathLen = candidate.length;\n\n    if (\n      prefixLen > bestPrefixLen ||\n      (prefixLen === bestPrefixLen && pathLen < bestPathLen)\n    ) {\n      bestPrefixLen = prefixLen;\n      bestPathLen = pathLen;\n      bestPath = candidate;\n    }\n  }\n\n  return bestPath;\n}\n\n/**\n * Compute the length of the common prefix between two directory paths,\n * measured in path segments (not raw characters).\n *\n * Example: \"a/b/c\" and \"a/b/d\" → 2 (common: \"a\", \"b\")\n */\nfunction commonPrefixLength(a: string, b: string): number {\n  if (a === \".\" && b === \".\") return 0;\n  const aParts = a === \".\" ? [] : a.split(\"/\");\n  const bParts = b === \".\" ? [] : b.split(\"/\");\n  let count = 0;\n  const len = Math.min(aParts.length, bParts.length);\n  for (let i = 0; i < len; i++) {\n    if (aParts[i] === bParts[i]) {\n      count++;\n    } else {\n      break;\n    }\n  }\n  return count;\n}\n","/**\n * Main vault indexing orchestrator.\n *\n * Indexes an entire Obsidian vault (or any markdown knowledge base), following\n * symlinks, deduplicating files by inode, parsing wikilinks, and computing\n * per-file health metrics (orphan detection, dead links).\n *\n * Key differences from the project indexer (indexer/sync.ts):\n *  - Follows symbolic links (project indexer skips them)\n *  - Deduplicates files with the same inode (same content reachable via multiple paths)\n *  - Parses [[wikilinks]] and builds a directed link graph\n *  - Resolves wikilinks using Obsidian's shortest-match algorithm\n *  - Computes health metrics per file: inbound/outbound link counts, dead links, orphans\n */\n\nimport { readFileSync } from \"node:fs\";\nimport { basename } from \"node:path\";\nimport type {\n  StorageBackend,\n  VaultFileRow,\n  VaultAliasRow,\n  VaultLinkRow,\n  VaultHealthRow,\n  VaultNameEntry,\n  ChunkRow,\n} from \"../../storage/interface.js\";\nimport { chunkMarkdown } from \"../chunker.js\";\nimport { sha256File, chunkId, yieldToEventLoop } from \"../indexer/helpers.js\";\nimport { walkVaultMdFiles } from \"./walk.js\";\nimport { deduplicateByInode } from \"./deduplicate.js\";\nimport { parseLinks } from \"./parse-links.js\";\nimport { buildNameIndex } from \"./name-index.js\";\nimport { resolveWikilink } from \"./resolve.js\";\nimport type { VaultIndexResult } from \"./types.js\";\n\n/** Number of files to process before yielding to the event loop. */\nconst VAULT_YIELD_EVERY = 1;\n\n/**\n * Index an entire Obsidian vault (or markdown knowledge base) using the\n * async StorageBackend interface.\n *\n * Steps:\n *  1. Walk vault root, following symlinks.\n *  2. Deduplicate by inode — each unique file is indexed once.\n *  3. Build a name index for wikilink resolution.\n *  4. For each canonical file:\n *     a. SHA-256 hash for change detection — skip unchanged files.\n *     b. Read content, chunk with chunkMarkdown().\n *     c. Insert chunks into backend (memory_chunks and memory_fts).\n *     d. Upsert vault_files row.\n *  5. Record aliases in vault_aliases.\n *  6. Rebuild vault_name_index table.\n *  7. Rebuild vault_links:\n *     a. Parse [[wikilinks]] from each canonical file.\n *     b. Resolve each link with resolveWikilink().\n *     c. Insert into vault_links.\n *  8. Compute and upsert health metrics (vault_health).\n *  9. Return statistics.\n *\n * @param backend         StorageBackend to write to.\n * @param vaultProjectId  Registry project ID for the vault \"project\".\n * @param vaultRoot       Absolute path to the vault root directory.\n */\nexport async function indexVault(\n  backend: StorageBackend,\n  vaultProjectId: number,\n  vaultRoot: string,\n): Promise<VaultIndexResult> {\n  const startTime = Date.now();\n\n  const result: VaultIndexResult = {\n    filesIndexed: 0,\n    chunksCreated: 0,\n    filesSkipped: 0,\n    aliasesRecorded: 0,\n    linksExtracted: 0,\n    deadLinksFound: 0,\n    orphansFound: 0,\n    elapsed: 0,\n  };\n\n  // Step 1: Walk vault, collecting all .md files (follows symlinks)\n  const allFiles = walkVaultMdFiles(vaultRoot);\n\n  // Step 2: Deduplicate by inode\n  const inodeGroups = deduplicateByInode(allFiles);\n\n  // Step 3: Build name index (from all files including aliases, for resolution)\n  const nameIndex = buildNameIndex(allFiles);\n\n  // Step 4: Index each canonical file\n  await yieldToEventLoop();\n  let filesSinceYield = 0;\n\n  for (const group of inodeGroups) {\n    if (filesSinceYield >= VAULT_YIELD_EVERY) {\n      await yieldToEventLoop();\n      filesSinceYield = 0;\n    }\n    filesSinceYield++;\n\n    const { canonical } = group;\n\n    let content: string;\n    try {\n      content = readFileSync(canonical.absPath, \"utf8\");\n    } catch {\n      result.filesSkipped++;\n      continue;\n    }\n\n    const hash = sha256File(content);\n\n    // Change detection: skip if hash is unchanged\n    const existing = await backend.getVaultFile(canonical.vaultRelPath);\n    if (existing?.hash === hash) {\n      result.filesSkipped++;\n      continue;\n    }\n\n    // Delete old chunks for this vault path\n    await backend.deleteChunksForFile(vaultProjectId, canonical.vaultRelPath);\n\n    // Chunk the content\n    const chunks = chunkMarkdown(content);\n    const updatedAt = Date.now();\n\n    // Extract title from first H1 heading or filename\n    const titleMatch = /^#\\s+(.+)$/m.exec(content);\n    const title = titleMatch\n      ? titleMatch[1]!.trim()\n      : basename(canonical.vaultRelPath, \".md\");\n\n    // Build chunk rows\n    const chunkRows: ChunkRow[] = [];\n    for (let i = 0; i < chunks.length; i++) {\n      const chunk = chunks[i]!;\n      const id = chunkId(\n        vaultProjectId,\n        canonical.vaultRelPath,\n        i,\n        chunk.startLine,\n        chunk.endLine,\n      );\n      chunkRows.push({\n        id,\n        projectId: vaultProjectId,\n        source: \"vault\",\n        tier: \"topic\",\n        path: canonical.vaultRelPath,\n        startLine: chunk.startLine,\n        endLine: chunk.endLine,\n        hash: chunk.hash,\n        text: chunk.text,\n        updatedAt,\n      });\n    }\n\n    if (chunkRows.length > 0) {\n      await backend.insertChunks(chunkRows);\n    }\n\n    // Upsert vault file record\n    const vaultFileRow: VaultFileRow = {\n      vaultPath: canonical.vaultRelPath,\n      inode: canonical.inode,\n      device: canonical.device,\n      hash,\n      title,\n      indexedAt: updatedAt,\n    };\n    await backend.upsertVaultFile(vaultFileRow);\n\n    result.filesIndexed++;\n    result.chunksCreated += chunks.length;\n  }\n\n  // Step 5: Record aliases in vault_aliases\n  await yieldToEventLoop();\n\n  const allAliases: VaultAliasRow[] = [];\n  for (const group of inodeGroups) {\n    for (const alias of group.aliases) {\n      allAliases.push({\n        vaultPath: alias.vaultRelPath,\n        canonicalPath: group.canonical.vaultRelPath,\n        inode: alias.inode,\n        device: alias.device,\n      });\n      result.aliasesRecorded++;\n    }\n  }\n\n  const canonicalPaths = new Set(inodeGroups.map((g) => g.canonical.vaultRelPath));\n  for (const canonPath of canonicalPaths) {\n    await backend.deleteVaultAliases(canonPath);\n  }\n  if (allAliases.length > 0) {\n    await backend.upsertVaultAliases(allAliases);\n  }\n\n  // Step 6: Rebuild vault_name_index\n  await yieldToEventLoop();\n\n  const nameEntries: VaultNameEntry[] = [];\n  for (const [name, paths] of nameIndex) {\n    for (const path of paths) {\n      nameEntries.push({ name, vaultPath: path });\n    }\n  }\n  await backend.replaceNameIndex(nameEntries);\n\n  // Step 7: Rebuild vault_links\n  await yieldToEventLoop();\n\n  const linkRows: VaultLinkRow[] = [];\n  const allSourcePaths: string[] = [];\n\n  let linkParseYield = 0;\n  for (const group of inodeGroups) {\n    if (linkParseYield++ % VAULT_YIELD_EVERY === 0) {\n      await yieldToEventLoop();\n    }\n\n    const { canonical } = group;\n    allSourcePaths.push(canonical.vaultRelPath);\n\n    let content: string;\n    try {\n      content = readFileSync(canonical.absPath, \"utf8\");\n    } catch {\n      continue;\n    }\n\n    const parsedLinks = parseLinks(content);\n    for (const link of parsedLinks) {\n      const target = resolveWikilink(link.raw, nameIndex, canonical.vaultRelPath);\n      let linkType: string;\n      if (link.isMdLink) {\n        linkType = link.isEmbed ? \"md-embed\" : \"md-link\";\n      } else {\n        linkType = link.isEmbed ? \"embed\" : \"wikilink\";\n      }\n      linkRows.push({\n        sourcePath: canonical.vaultRelPath,\n        targetRaw: link.raw,\n        targetPath: target,\n        linkType,\n        lineNumber: link.lineNumber,\n        confidence: \"EXTRACTED\",\n      });\n    }\n  }\n\n  // Replace all links for all sources in batches of 500\n  const LINK_BATCH_SIZE = 500;\n  for (let i = 0; i < allSourcePaths.length; i += LINK_BATCH_SIZE) {\n    const batchSources = allSourcePaths.slice(i, i + LINK_BATCH_SIZE);\n    const batchLinks = linkRows.filter((r) => batchSources.includes(r.sourcePath));\n    await backend.replaceLinksForSources(batchSources, batchLinks);\n    await yieldToEventLoop();\n  }\n\n  result.linksExtracted = linkRows.length;\n  result.deadLinksFound = linkRows.filter((r) => r.targetPath === null).length;\n\n  // Step 8: Compute and upsert vault_health metrics\n  await yieldToEventLoop();\n\n  const outboundMap = new Map<string, number>();\n  const deadMap = new Map<string, number>();\n  const inboundMap = new Map<string, number>();\n\n  for (const row of linkRows) {\n    outboundMap.set(row.sourcePath, (outboundMap.get(row.sourcePath) ?? 0) + 1);\n    if (row.targetPath === null) {\n      deadMap.set(row.sourcePath, (deadMap.get(row.sourcePath) ?? 0) + 1);\n    } else {\n      inboundMap.set(row.targetPath, (inboundMap.get(row.targetPath) ?? 0) + 1);\n    }\n  }\n\n  const computedAt = Date.now();\n  let orphanCount = 0;\n\n  const HEALTH_BATCH_SIZE = 500;\n  for (let i = 0; i < inodeGroups.length; i += HEALTH_BATCH_SIZE) {\n    const batch = inodeGroups.slice(i, i + HEALTH_BATCH_SIZE);\n    const healthRows: VaultHealthRow[] = batch.map((group) => {\n      const path = group.canonical.vaultRelPath;\n      const inbound = inboundMap.get(path) ?? 0;\n      const outbound = outboundMap.get(path) ?? 0;\n      const dead = deadMap.get(path) ?? 0;\n      const isOrphan = inbound === 0;\n      if (isOrphan) orphanCount++;\n      return {\n        vaultPath: path,\n        inboundCount: inbound,\n        outboundCount: outbound,\n        deadLinkCount: dead,\n        isOrphan,\n        computedAt,\n      };\n    });\n    await backend.upsertVaultHealth(healthRows);\n    await yieldToEventLoop();\n  }\n\n  result.orphansFound = orphanCount;\n  result.elapsed = Date.now() - startTime;\n\n  return 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package/dist/{work-queue-worker-BcDGAcF3.mjs → work-queue-worker-228XjABm.mjs}

@@ -1,10 +1,9 @@
-import { t as __exportAll } from "./rolldown-runtime-95iHPtFO.mjs";
-import { n as openFederation } from "./db-CYmBWcjh.mjs";
-import { l as performScan, n as applyContinue, o as extractAndStoreTriples$1 } from "./checkpoint-block-D3rm4dAJ.mjs";
-import { O as storageBackend, t as daemonConfig, u as registryDb } from "./state-DTvy-jRB.mjs";
-import { t as detectTopicShift } from "./detector-BU-bsDXs.mjs";
+import { t as openFederation } from "./db-a1ixZQjr.mjs";
+import { l as performScan, n as applyContinue, o as extractAndStoreTriples$1 } from "./checkpoint-block-DKYxCkBL.mjs";
+import { D as storageBackend, t as daemonConfig, u as registryDb } from "./state-WaXhLr6R.mjs";
+import { t as detectTopicShift } from "./detector--Gg5JRN5.mjs";
 import { existsSync, mkdirSync, readFileSync, readdirSync, renameSync, statSync, unlinkSync, writeFileSync } from "node:fs";
-import { homedir } from "node:os";
+import { homedir, tmpdir } from "node:os";
 import { basename, dirname, join } from "node:path";
 import { randomUUID } from "node:crypto";
 import { copyFileSync as copyFileSync$1, existsSync as existsSync$1, linkSync as linkSync$1, mkdirSync as mkdirSync$1, readFileSync as readFileSync$1, readdirSync as readdirSync$1, renameSync as renameSync$1, writeFileSync as writeFileSync$1 } from "fs";
@@ -1576,6 +1575,227 @@ async function handleSessionSummary(payload) {
 	process.stderr.write("[session-summary] Done.\n");
 }
 
+//#endregion
+//#region src/daemon/templates/context-handover-prompt.ts
+function buildContextHandoverPrompt(params) {
+	const { turns, gitLog, cwd, previousHandover } = params;
+	const turnsSection = turns.length > 0 ? turns.join("\n\n") : "(No turns extracted)";
+	const gitSection = gitLog.trim() || "(No git commits during this session)";
+	return `This session is approaching a context-window compaction. Write the \
+handover that would let a successor continue WITHOUT re-reading this \
+conversation and WITHOUT asking the user to repeat themselves.
+
+Project directory: ${cwd}
+${previousHandover ? `\nA PREVIOUS HANDOVER already exists for this session (from an earlier, \
+lower threshold). Carry it forward — start your response with a one-line \
+pointer to it ("Carries forward from the previous handover, which stays for \
+its detail.") and then write only what has happened SINCE it that a compact \
+would also lose. Do not re-derive or repeat what it already covered.\n\n\
+PREVIOUS HANDOVER:\n${previousHandover}\n` : ""}
+SCOPING RULE — the single most important instruction here: this is a DIFF \
+against everything already durable, not a summary of the session. Assume \
+the successor can and will read git history, the issue tracker, and any \
+notes files themselves. Do NOT restate anything recoverable there — no file \
+inventories, no "implemented X" restatements, no chronology of commands run. \
+Write down ONLY what existed exclusively in this conversation and would \
+otherwise be gone: the reasoning, not the result.
+
+Write ONLY the sections below that this session actually has content for — \
+omit a section entirely rather than writing "none" or padding it:
+
+WHERE THIS SESSION ENDED — the concrete state right now: what is verified \
+working (tests green, tree clean, etc.) versus merely attempted, any branch \
+or working-tree state that isn't obvious from git status alone (e.g. a \
+detached HEAD, an intentionally uncommitted change, a stash).
+
+WHAT CLOSED — each item paired with the evidence that closed it, not just \
+the claim that it did.
+
+WHAT IS FILED AND STILL OPEN — each with its next concrete step or who/what \
+it is waiting on.
+
+DECISIONS & REASONING — choices actually made, each with why this way and \
+not another way.
+
+REJECTED ALTERNATIVES — approaches considered and set aside, and why. An \
+alternative without a reason is not worth recording.
+
+NEGATIVE RESULTS — something investigated that turned out NOT to be the \
+answer, kept WITH the reasoning that ruled it out (e.g. "X looked like the \
+cause — it wasn't; the actual mechanism was Y"). Without the reasoning \
+attached, a successor re-investigates the same dead end.
+
+TRAPS — anything discovered that is invisible from the repo alone and would \
+otherwise bite a successor immediately (a required manual step, an ordering \
+constraint, a state that looks fine but isn't).
+
+CRITICAL VALUES — any specific id, path, URL, credential name, version \
+number, or configuration value that appeared in conversation and whose loss \
+would force someone to go find it again.
+
+THE FEW THINGS THAT MATTER MOST, IF NOTHING ELSE IS READ — at most 3 bullets. \
+Forces a priority judgement; do not pad this to fill space.
+
+Format your response as markdown with those section headers (only the ones \
+you have content for), no other structure.
+
+---
+
+CONVERSATION:
+${turnsSection}
+
+GIT COMMITS:
+${gitSection}`;
+}
+
+//#endregion
+//#region src/hooks/ts/lib/context-handover-cache.ts
+/**
+* context-handover-cache.ts — the well-known file where the threshold-
+* triggered pre-compaction handover (see ../../../daemon/context-handover-
+* worker.ts) is written, and where context-compression-hook.ts looks for it
+* at compaction time.
+*
+* Deliberately dependency-light (fs/os/path only). The daemon worker that
+* WRITES this file needs the heavier machinery in session-summary-worker.ts
+* (spawning Claude, git log, etc.), but the PreCompact hook that READS it
+* runs as a short-lived process on every compaction and must not drag in
+* daemon state, database pools, or anything else that module graph carries —
+* this file is the shared seam so neither side has to.
+*/
+function contextHandoverCachePath(sessionId) {
+	return join(tmpdir(), `pai-context-handover-${sessionId}.json`);
+}
+function readContextHandoverCache(sessionId) {
+	const path = contextHandoverCachePath(sessionId);
+	if (!existsSync(path)) return null;
+	try {
+		return JSON.parse(readFileSync(path, "utf-8"));
+	} catch {
+		return null;
+	}
+}
+function writeContextHandoverCache(cache) {
+	writeFileSync(contextHandoverCachePath(cache.sessionId), JSON.stringify(cache, null, 2), "utf-8");
+}
+
+//#endregion
+//#region src/daemon/context-handover-worker.ts
+/**
+* context-handover-worker.ts — the threshold-triggered pre-compaction
+* handover.
+*
+* `session-summary-worker.ts` already spawns a model to write session notes,
+* but only from the PreCompact hook itself — which fires at the compaction
+* boundary, far too late to be injected INTO that same compaction's
+* post-compact context. This worker runs earlier, off a token-count
+* threshold (see ../hooks/ts/lib/context-fill.ts), so a model-written
+* handover already exists in a cache file by the time compaction happens.
+*
+* Deliberately narrow: this does not write a session note, does not touch
+* the session-summary cooldown file, and does not run KG extraction. It
+* writes one thing — a cache file the PreCompact hook can read — because its
+* only job is to exist before compaction does, not to duplicate what
+* session-summary-worker already does well.
+*
+* The prompt itself (see templates/context-handover-prompt.ts) treats the
+* handover as a DIFF against everything already durable — git, the tracker,
+* the notes — not a session summary, and a refresh run carries the previous
+* cached handover forward rather than overwriting it.
+*/
+/** How much of the tail of the transcript to feed the summarizer. Generous —
+*  this runs at most twice per session, not on every tool call. */
+const MAX_TURN_CHARS = 15e4;
+/** Max turns to include (a hard floor even if MAX_TURN_CHARS is not hit). */
+const MAX_TURNS = 120;
+/**
+* Interleaved "User:"/"Assistant:" turns, oldest-kept-from-the-end so a long
+* transcript is truncated to its most recent content rather than its
+* earliest. Unlike session-summary-worker's extractFromJsonl (which keeps
+* only user messages, because a session note doesn't need the assistant's
+* own reasoning) this keeps BOTH sides — the whole point of this prompt is
+* the assistant's reasoning, which lives in assistant turns.
+*/
+function extractTurns(jsonlPath) {
+	let raw;
+	try {
+		raw = readFileSync(jsonlPath, "utf-8");
+	} catch {
+		return [];
+	}
+	if (raw.length > MAX_TURN_CHARS) {
+		const truncPoint = raw.indexOf("\n", raw.length - MAX_TURN_CHARS);
+		raw = truncPoint >= 0 ? raw.slice(truncPoint + 1) : raw.slice(-MAX_TURN_CHARS);
+	}
+	const turns = [];
+	for (const line of raw.trim().split("\n")) {
+		if (!line.trim()) continue;
+		let entry;
+		try {
+			entry = JSON.parse(line);
+		} catch {
+			continue;
+		}
+		if (entry.type === "user") {
+			const msg = entry.message;
+			const text = contentToText$2(msg?.content);
+			if (text && text.length >= 3 && !text.startsWith("<system-reminder>")) turns.push(`User: ${text.slice(0, 2e3)}`);
+		} else if (entry.type === "assistant") {
+			const msg = entry.message;
+			const text = contentToText$2(msg?.content);
+			if (text && text.length >= 3) turns.push(`Assistant: ${text.slice(0, 4e3)}`);
+		}
+	}
+	return turns.slice(-MAX_TURNS);
+}
+/**
+* Process a `context-handover` work item. Best-effort throughout: a failed
+* or empty summarizer run logs and returns without writing a cache file —
+* never overwrites a previously good cache with nothing, and never throws
+* (the work queue would otherwise retry a job whose only cost is an LLM
+* call nobody is waiting on).
+*/
+async function handleContextHandover(payload) {
+	const { cwd, sessionId, transcriptPath, threshold, urgent } = payload;
+	if (!cwd || !sessionId) {
+		process.stderr.write("[context-handover] payload missing cwd or sessionId — skipping.\n");
+		return;
+	}
+	process.stderr.write(`[context-handover] Starting for ${cwd} (session=${sessionId}, threshold=${threshold}${urgent ? ", urgent" : ""}).\n`);
+	let jsonlPath = transcriptPath && existsSync(transcriptPath) ? transcriptPath : null;
+	if (!jsonlPath) jsonlPath = findLatestJsonl(cwd);
+	if (!jsonlPath) {
+		process.stderr.write("[context-handover] No transcript found — skipping.\n");
+		return;
+	}
+	const turns = extractTurns(jsonlPath);
+	if (turns.length === 0) {
+		process.stderr.write("[context-handover] No turns extracted — skipping.\n");
+		return;
+	}
+	const prompt = buildContextHandoverPrompt({
+		turns,
+		gitLog: await getGitContext(cwd),
+		cwd,
+		previousHandover: readContextHandoverCache(sessionId)?.summary
+	});
+	process.stderr.write(`[context-handover] Sending ${prompt.length} char prompt to sonnet...\n`);
+	const summary = await spawnSummarizer(prompt, "sonnet");
+	if (!summary || !summary.trim()) {
+		process.stderr.write("[context-handover] sonnet produced no output — leaving any existing cache untouched.\n");
+		return;
+	}
+	writeContextHandoverCache({
+		sessionId,
+		cwd,
+		threshold,
+		generatedAt: (/* @__PURE__ */ new Date()).toISOString(),
+		model: "sonnet",
+		summary: summary.trim()
+	});
+	process.stderr.write(`[context-handover] Wrote cache for session ${sessionId} (${summary.length} chars).\n`);
+}
+
 //#endregion
 //#region src/daemon/topic-detect-worker.ts
 /**
@@ -1708,18 +1928,15 @@ async function handleTopicDetect(payload) {
 * Handles 'session-end' work items by reading the transcript, extracting
 * work summaries, updating the session note, and updating TODO.md.
 * Handles 'session-summary' items by spawning Haiku for AI-powered note generation.
+* Handles 'context-handover' items by spawning Sonnet to write the
+* threshold-triggered pre-compaction reasoning handover (see
+* context-handover-worker.ts and hooks/ts/lib/context-fill.ts).
 * Handles 'registry-scan' items by running performScan() against the registry DB.
 *
 * Handles 'topic-detect' items by running BM25-based topic shift detection.
 * Other item types (note-update, todo-update) are stubs — they log and
 * complete immediately, ready for future expansion.
 */
-var work_queue_worker_exports = /* @__PURE__ */ __exportAll({
-	enqueueRegistryScan: () => enqueueRegistryScan,
-	notifyNewWork: () => notifyNewWork,
-	startWorker: () => startWorker,
-	stopWorker: () => stopWorker
-});
 const WORKER_INTERVAL_MS = 5e3;
 const HOUSEKEEPING_INTERVAL_MS = 600 * 1e3;
 let workerTimer = null;
@@ -1773,6 +1990,9 @@ async function processNextItem() {
 			case "session-summary":
 				await handleSessionSummary(item.payload);
 				break;
+			case "context-handover":
+				await handleContextHandover(item.payload);
+				break;
 			case "topic-detect":
 				await handleTopicDetect(item.payload);
 				break;
@@ -1947,5 +2167,5 @@ function extractWorkFromTranscript(lines) {
 }
 
 //#endregion
-export { enqueue as a, work_queue_worker_exports as i, startWorker as n, getStats as o, stopWorker as r, loadQueue as s, notifyNewWork as t };
-//# sourceMappingURL=work-queue-worker-BcDGAcF3.mjs.map
+export { enqueue as a, stopWorker as i, notifyNewWork as n, getStats as o, startWorker as r, loadQueue as s, enqueueRegistryScan as t };
+//# sourceMappingURL=work-queue-worker-228XjABm.mjs.map