@tekmidian/pai 0.9.0 → 0.9.2

package/dist/{trace-CRx9lPuc.mjs.map → trace-C2XrzssW.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"trace-CRx9lPuc.mjs","names":[],"sources":["../src/graph/trace.ts"],"sourcesContent":["/**\n * trace.ts — graph_trace endpoint handler\n *\n * Given a topic/keyword query, searches vault notes for appearances of that topic\n * and returns a chronological timeline showing how the idea evolved over time.\n */\n\nimport type { StorageBackend } from \"../storage/interface.js\";\n\n// ---------------------------------------------------------------------------\n// Public param / result types\n// ---------------------------------------------------------------------------\n\nexport interface GraphTraceParams {\n  query: string;\n  project_id: number;\n  max_results?: number;\n  lookback_days?: number;\n}\n\nexport interface TraceEntry {\n  vault_path: string;\n  title: string;\n  folder: string;\n  indexed_at: number;\n  snippet: string;\n  dominant_type: string;\n}\n\nexport interface TraceConnection {\n  from_path: string;\n  to_path: string;\n  type: \"temporal\" | \"wikilink\";\n}\n\nexport interface GraphTraceResult {\n  query: string;\n  entries: TraceEntry[];\n  connections: TraceConnection[];\n  time_span: { from: number; to: number };\n}\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\nfunction folderFromPath(vaultPath: string): string {\n  const lastSlash = vaultPath.lastIndexOf(\"/\");\n  return lastSlash === -1 ? \"\" : vaultPath.slice(0, lastSlash);\n}\n\nfunction extractSnippet(text: string, query: string): string {\n  const lowerText = text.toLowerCase();\n  const lowerQuery = query.toLowerCase();\n  const idx = lowerText.indexOf(lowerQuery);\n  if (idx === -1) {\n    return text.slice(0, 160).trimEnd() + (text.length > 160 ? \"…\" : \"\");\n  }\n\n  const CONTEXT = 70;\n  const start = Math.max(0, idx - CONTEXT);\n  const end = Math.min(text.length, idx + query.length + CONTEXT);\n\n  let snippet = text.slice(start, end).replace(/\\s+/g, \" \").trim();\n  if (start > 0) snippet = \"…\" + snippet;\n  if (end < text.length) snippet = snippet + \"…\";\n\n  return snippet;\n}\n\n// ---------------------------------------------------------------------------\n// Main handler\n// ---------------------------------------------------------------------------\n\nexport async function handleGraphTrace(\n  backend: StorageBackend,\n  params: GraphTraceParams\n): Promise<GraphTraceResult> {\n  const query = (params.query ?? \"\").trim();\n  if (!query) {\n    return { query: \"\", entries: [], connections: [], time_span: { from: 0, to: 0 } };\n  }\n\n  const maxResults = params.max_results ?? 30;\n  const lookbackDays = params.lookback_days ?? 365;\n  const cutoffTimestamp = Math.floor(Date.now() / 1000) - lookbackDays * 86400;\n\n  // ---------------------------------------------------------------------------\n  // Step 1: Collect matching vault paths via multiple search strategies\n  // ---------------------------------------------------------------------------\n\n  const matchedPaths = new Map<string, string>(); // path → best snippet text\n\n  // Strategy A: title / alias match in vault_name_index\n  try {\n    const namePaths = await backend.searchVaultNameIndex(query, 100);\n    for (const vaultPath of namePaths) {\n      if (!matchedPaths.has(vaultPath)) {\n        matchedPaths.set(vaultPath, \"\");\n      }\n    }\n  } catch {\n    // vault_name_index may not exist in all schema versions\n  }\n\n  // Strategy B: content search in memory_chunks\n  try {\n    const chunkRows = await backend.searchChunksByText(params.project_id, query, 200);\n    for (const row of chunkRows) {\n      if (!matchedPaths.has(row.path)) {\n        matchedPaths.set(row.path, row.text);\n      } else if (!matchedPaths.get(row.path)) {\n        matchedPaths.set(row.path, row.text);\n      }\n    }\n  } catch {\n    // Best-effort — continue with what we have\n  }\n\n  if (matchedPaths.size === 0) {\n    return { query, entries: [], connections: [], time_span: { from: 0, to: 0 } };\n  }\n\n  // ---------------------------------------------------------------------------\n  // Step 2: Fetch vault_files metadata for all matched paths, filtered by cutoff\n  // ---------------------------------------------------------------------------\n\n  const allPaths = Array.from(matchedPaths.keys());\n  let fileRows: Array<{ vaultPath: string; title: string | null; indexedAt: number }> = [];\n  try {\n    fileRows = await backend.getVaultFilesByPathsAfter(allPaths, cutoffTimestamp * 1000);\n    // Sort chronologically\n    fileRows.sort((a, b) => a.indexedAt - b.indexedAt);\n  } catch {\n    return { query, entries: [], connections: [], time_span: { from: 0, to: 0 } };\n  }\n\n  if (fileRows.length === 0) {\n    return { query, entries: [], connections: [], time_span: { from: 0, to: 0 } };\n  }\n\n  // ---------------------------------------------------------------------------\n  // Step 3: Build TraceEntry array\n  // ---------------------------------------------------------------------------\n\n  const entries: TraceEntry[] = fileRows.slice(0, maxResults).map((row) => {\n    const fileName = row.vaultPath.split(\"/\").pop() ?? row.vaultPath;\n    const title = row.title ?? fileName.replace(/\\.md$/i, \"\");\n    const chunkText = matchedPaths.get(row.vaultPath) ?? \"\";\n    const snippet = extractSnippet(chunkText, query);\n\n    return {\n      vault_path: row.vaultPath,\n      title,\n      folder: folderFromPath(row.vaultPath),\n      indexed_at: row.indexedAt,\n      snippet,\n      dominant_type: \"unknown\",\n    };\n  });\n\n  if (entries.length === 0) {\n    return { query, entries: [], connections: [], time_span: { from: 0, to: 0 } };\n  }\n\n  // ---------------------------------------------------------------------------\n  // Step 4: Build connections\n  // ---------------------------------------------------------------------------\n\n  const connections: TraceConnection[] = [];\n  const entryPathSet = new Set(entries.map((e) => e.vault_path));\n\n  // Temporal edges: consecutive entries (oldest → next)\n  for (let i = 0; i < entries.length - 1; i++) {\n    connections.push({\n      from_path: entries[i].vault_path,\n      to_path: entries[i + 1].vault_path,\n      type: \"temporal\",\n    });\n  }\n\n  // Wikilink edges\n  try {\n    const entryPaths = entries.map(e => e.vault_path);\n    const linkRows = await backend.getVaultLinksFromPaths(entryPaths);\n\n    const wikiEdgeKeys = new Set<string>();\n    for (const row of linkRows) {\n      if (!row.targetPath) continue;\n      if (!entryPathSet.has(row.targetPath)) continue;\n\n      const key = `${row.sourcePath}|||${row.targetPath}`;\n      if (wikiEdgeKeys.has(key)) continue;\n      wikiEdgeKeys.add(key);\n\n      connections.push({\n        from_path: row.sourcePath,\n        to_path: row.targetPath,\n        type: \"wikilink\",\n      });\n    }\n  } catch {\n    // vault_links may not exist — temporal edges are sufficient\n  }\n\n  // ---------------------------------------------------------------------------\n  // Step 5: Compute time span\n  // ---------------------------------------------------------------------------\n\n  const timestamps = entries.map((e) => e.indexed_at).filter((t) => t > 0);\n  const timeFrom = timestamps.length > 0 ? Math.min(...timestamps) : 0;\n  const timeTo = timestamps.length > 0 ? 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+{"version":3,"file":"trace-C2XrzssW.mjs","names":[],"sources":["../src/graph/trace.ts"],"sourcesContent":["/**\n * trace.ts — graph_trace endpoint handler\n *\n * Given a topic/keyword query, searches vault notes for appearances of that topic\n * and returns a chronological timeline showing how the idea evolved over time.\n */\n\nimport type { StorageBackend } from \"../storage/interface.js\";\n\n// ---------------------------------------------------------------------------\n// Public param / result types\n// ---------------------------------------------------------------------------\n\nexport interface GraphTraceParams {\n  query: string;\n  project_id: number;\n  max_results?: number;\n  lookback_days?: number;\n}\n\nexport interface TraceEntry {\n  vault_path: string;\n  title: string;\n  folder: string;\n  indexed_at: number;\n  snippet: string;\n  dominant_type: string;\n}\n\nexport interface TraceConnection {\n  from_path: string;\n  to_path: string;\n  type: \"temporal\" | \"wikilink\";\n}\n\nexport interface GraphTraceResult {\n  query: string;\n  entries: TraceEntry[];\n  connections: TraceConnection[];\n  time_span: { from: number; to: number };\n}\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\nfunction folderFromPath(vaultPath: string): string {\n  const lastSlash = vaultPath.lastIndexOf(\"/\");\n  return lastSlash === -1 ? \"\" : vaultPath.slice(0, lastSlash);\n}\n\nfunction extractSnippet(text: string, query: string): string {\n  const lowerText = text.toLowerCase();\n  const lowerQuery = query.toLowerCase();\n  const idx = lowerText.indexOf(lowerQuery);\n  if (idx === -1) {\n    return text.slice(0, 160).trimEnd() + (text.length > 160 ? \"…\" : \"\");\n  }\n\n  const CONTEXT = 70;\n  const start = Math.max(0, idx - CONTEXT);\n  const end = Math.min(text.length, idx + query.length + CONTEXT);\n\n  let snippet = text.slice(start, end).replace(/\\s+/g, \" \").trim();\n  if (start > 0) snippet = \"…\" + snippet;\n  if (end < text.length) snippet = snippet + \"…\";\n\n  return snippet;\n}\n\n// ---------------------------------------------------------------------------\n// Main handler\n// ---------------------------------------------------------------------------\n\nexport async function handleGraphTrace(\n  backend: StorageBackend,\n  params: GraphTraceParams\n): Promise<GraphTraceResult> {\n  const query = (params.query ?? \"\").trim();\n  if (!query) {\n    return { query: \"\", entries: [], connections: [], time_span: { from: 0, to: 0 } };\n  }\n\n  const maxResults = params.max_results ?? 30;\n  const lookbackDays = params.lookback_days ?? 365;\n  const cutoffTimestamp = Math.floor(Date.now() / 1000) - lookbackDays * 86400;\n\n  // ---------------------------------------------------------------------------\n  // Step 1: Collect matching vault paths via multiple search strategies\n  // ---------------------------------------------------------------------------\n\n  const matchedPaths = new Map<string, string>(); // path → best snippet text\n\n  // Strategy A: title / alias match in vault_name_index\n  try {\n    const namePaths = await backend.searchVaultNameIndex(query, 100);\n    for (const vaultPath of namePaths) {\n      if (!matchedPaths.has(vaultPath)) {\n        matchedPaths.set(vaultPath, \"\");\n      }\n    }\n  } catch {\n    // vault_name_index may not exist in all schema versions\n  }\n\n  // Strategy B: content search in memory_chunks\n  try {\n    const chunkRows = await backend.searchChunksByText(params.project_id, query, 200);\n    for (const row of chunkRows) {\n      if (!matchedPaths.has(row.path)) {\n        matchedPaths.set(row.path, row.text);\n      } else if (!matchedPaths.get(row.path)) {\n        matchedPaths.set(row.path, row.text);\n      }\n    }\n  } catch {\n    // Best-effort — continue with what we have\n  }\n\n  if (matchedPaths.size === 0) {\n    return { query, entries: [], connections: [], time_span: { from: 0, to: 0 } };\n  }\n\n  // ---------------------------------------------------------------------------\n  // Step 2: Fetch vault_files metadata for all matched paths, filtered by cutoff\n  // ---------------------------------------------------------------------------\n\n  const allPaths = Array.from(matchedPaths.keys());\n  let fileRows: Array<{ vaultPath: string; title: string | null; indexedAt: number }> = [];\n  try {\n    fileRows = await backend.getVaultFilesByPathsAfter(allPaths, cutoffTimestamp * 1000);\n    // Sort chronologically\n    fileRows.sort((a, b) => a.indexedAt - b.indexedAt);\n  } catch {\n    return { query, entries: [], connections: [], time_span: { from: 0, to: 0 } };\n  }\n\n  if (fileRows.length === 0) {\n    return { query, entries: [], connections: [], time_span: { from: 0, to: 0 } };\n  }\n\n  // ---------------------------------------------------------------------------\n  // Step 3: Build TraceEntry array\n  // ---------------------------------------------------------------------------\n\n  const entries: TraceEntry[] = fileRows.slice(0, maxResults).map((row) => {\n    const fileName = row.vaultPath.split(\"/\").pop() ?? 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Math.min(...timestamps) : 0;\n  const timeTo = timestamps.length > 0 ? 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package/dist/{vault-indexer-B-aJpRZC.mjs → vault-indexer-TTCl1QOL.mjs}

@@ -533,4 +533,4 @@ async function indexVault(backend, vaultProjectId, vaultRoot) {
 
 //#endregion
 export { indexVault };
-//# sourceMappingURL=vault-indexer-B-aJpRZC.mjs.map
+//# sourceMappingURL=vault-indexer-TTCl1QOL.mjs.map

package/dist/{vault-indexer-B-aJpRZC.mjs.map → vault-indexer-TTCl1QOL.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"vault-indexer-B-aJpRZC.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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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/{zettelkasten-DhBKZQHF.mjs → zettelkasten-BdaMzTGQ.mjs}

@@ -1,6 +1,6 @@
 import { a as generateEmbedding, n as cosineSimilarity, r as deserializeEmbedding } from "./embeddings-DGRAPAYb.mjs";
-import { t as zettelThemes } from "./themes-BvYF0W8T.mjs";
-import { n as saveQueryResult } from "./query-feedback-Dv43XKHM.mjs";
+import { t as zettelThemes } from "./themes-9jxFn3Rf.mjs";
+import { n as saveQueryResult } from "./query-feedback-CQSumXDy.mjs";
 import { basename, dirname } from "node:path";
 
 //#region src/zettelkasten/explore.ts
@@ -1060,4 +1060,4 @@ async function zettelCommunities(backend, opts) {
 
 //#endregion
 export { zettelCommunities, zettelConverse, zettelExplore, zettelGodNotes, zettelHealth, zettelSuggest, zettelSurprise, zettelThemes };
-//# sourceMappingURL=zettelkasten-DhBKZQHF.mjs.map
+//# sourceMappingURL=zettelkasten-BdaMzTGQ.mjs.map