@tekmidian/pai 0.4.0 → 0.5.1

package/dist/{vault-indexer-Bo2aPSzP.mjs.map → vault-indexer-DXWs9pDn.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"vault-indexer-Bo2aPSzP.mjs","names":[],"sources":["../src/memory/vault-indexer.ts"],"sourcesContent":["/**\n * Vault indexer for the PAI federation memory engine.\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.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 { createHash } from \"node:crypto\";\nimport { readFileSync, statSync, readdirSync, existsSync } from \"node:fs\";\nimport { join, relative, basename, dirname, normalize } from \"node:path\";\nimport type { Database } from \"better-sqlite3\";\nimport { chunkMarkdown } from \"./chunker.js\";\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\nexport interface VaultFile {\n  absPath: string;\n  vaultRelPath: string;\n  inode: number;\n  device: number;\n}\n\nexport interface InodeGroup {\n  canonical: VaultFile;\n  aliases: VaultFile[];\n}\n\nexport interface ParsedLink {\n  raw: string;\n  alias: string | null;\n  lineNumber: number;\n  isEmbed: boolean;\n}\n\nexport interface VaultIndexResult {\n  filesIndexed: number;\n  chunksCreated: number;\n  filesSkipped: number;\n  aliasesRecorded: number;\n  linksExtracted: number;\n  deadLinksFound: number;\n  orphansFound: number;\n  elapsed: number;\n}\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\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/** Number of files to process before yielding to the event loop. */\nconst VAULT_YIELD_EVERY = 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// Utility\n// ---------------------------------------------------------------------------\n\nfunction sha256File(content: string): string {\n  return createHash(\"sha256\").update(content).digest(\"hex\");\n}\n\nfunction chunkId(\n  projectId: number,\n  path: string,\n  chunkIndex: number,\n  startLine: number,\n  endLine: number,\n): string {\n  return createHash(\"sha256\")\n    .update(`${projectId}:${path}:${chunkIndex}:${startLine}:${endLine}`)\n    .digest(\"hex\");\n}\n\nfunction yieldToEventLoop(): Promise<void> {\n  return new Promise((resolve) => setImmediate(resolve));\n}\n\n// ---------------------------------------------------------------------------\n// Vault directory walker (follows symlinks)\n// ---------------------------------------------------------------------------\n\n/**\n * Recursively collect all .md files under a vault root, following symlinks.\n *\n * Symlink-following behaviour:\n *  - Symbolic links to files: followed if the target is a .md file\n *  - Symbolic links to directories: followed with cycle detection via inode\n *\n * Cycle detection is based on the real inode of each visited directory.\n * Using the real stat (not lstat) ensures that symlinked dirs resolve to\n * their actual inode, preventing infinite loops.\n *\n * @param dir        Directory to scan.\n * @param vaultRoot  Absolute root of the vault (for computing vaultRelPath).\n * @param acc        Shared accumulator (mutated in place for early exit).\n * @param visited    Set of \"device:inode\" strings for visited directories.\n * @param depth      Current recursion depth.\n */\nexport function walkVaultMdFiles(\n  vaultRoot: string,\n  opts?: { maxFiles?: number; maxDepth?: number },\n): VaultFile[] {\n  const maxFiles = opts?.maxFiles ?? VAULT_MAX_FILES;\n  const maxDepth = opts?.maxDepth ?? VAULT_MAX_DEPTH;\n\n  const results: VaultFile[] = [];\n  const visitedDirs = new Set<string>();\n\n  function walk(dir: string, depth: number): void {\n    if (results.length >= maxFiles) return;\n    if (depth > maxDepth) return;\n\n    // Get the real inode of this directory (follows symlinks on the dir itself)\n    let dirStat: ReturnType<typeof statSync>;\n    try {\n      dirStat = statSync(dir);\n    } catch {\n      return; // Unreadable or broken symlink — skip\n    }\n\n    const dirKey = `${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// ---------------------------------------------------------------------------\n// Inode deduplication\n// ---------------------------------------------------------------------------\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// ---------------------------------------------------------------------------\n// Wikilink parser\n// ---------------------------------------------------------------------------\n\n/**\n * Parse all [[wikilinks]] and ![[embeds]] 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 *\n * @param content  Raw markdown file content.\n * @returns        Array of parsed links in document order.\n */\nexport function parseWikilinks(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  for (let lineIdx = 0; lineIdx < lines.length; lineIdx++) {\n    const line = lines[lineIdx]!;\n    const lineNumber = lineIdx + 1; // 1-indexed\n\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      // For frontmatter lines, mark as non-embed regardless of !\n      const isFrontmatter = lineIdx < frontmatterEnd;\n      links.push({\n        raw,\n        alias: alias?.trim() ?? null,\n        lineNumber,\n        isEmbed: isEmbed && !isFrontmatter,\n      });\n    }\n  }\n\n  return links;\n}\n\n// ---------------------------------------------------------------------------\n// Name index builder\n// ---------------------------------------------------------------------------\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// ---------------------------------------------------------------------------\n// Wikilink resolver\n// ---------------------------------------------------------------------------\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  // E.g. \"PAI/20-webseiten/_20-webseiten-master\" → \"_20-webseiten-master\"\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// ---------------------------------------------------------------------------\n// Main vault indexing orchestrator\n// ---------------------------------------------------------------------------\n\n/**\n * Index an entire Obsidian vault (or markdown knowledge base) into the\n * federation database.\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 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 db              Open federation database.\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  db: Database,\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  // ---------------------------------------------------------------------------\n  // Step 1: Walk vault, collecting all .md files (follows symlinks)\n  // ---------------------------------------------------------------------------\n\n  const allFiles = walkVaultMdFiles(vaultRoot);\n\n  // ---------------------------------------------------------------------------\n  // Step 2: Deduplicate by inode\n  // ---------------------------------------------------------------------------\n\n  const inodeGroups = deduplicateByInode(allFiles);\n\n  // ---------------------------------------------------------------------------\n  // Step 3: Build name index (from all files including aliases, for resolution)\n  // ---------------------------------------------------------------------------\n\n  const nameIndex = buildNameIndex(allFiles);\n\n  // ---------------------------------------------------------------------------\n  // Step 4: Prepare SQL statements\n  // ---------------------------------------------------------------------------\n\n  const selectFileHash = db.prepare(\n    \"SELECT hash FROM vault_files WHERE vault_path = ?\",\n  );\n\n  const deleteOldChunkIds = db.prepare(\n    \"SELECT id FROM memory_chunks WHERE project_id = ? AND path = ?\",\n  );\n\n  const deleteFts = db.prepare(\"DELETE FROM memory_fts WHERE id = ?\");\n\n  const deleteChunks = db.prepare(\n    \"DELETE FROM memory_chunks WHERE project_id = ? AND path = ?\",\n  );\n\n  const insertChunk = db.prepare(`\n    INSERT INTO memory_chunks (id, project_id, source, tier, path, start_line, end_line, hash, text, updated_at)\n    VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n  `);\n\n  const insertFts = db.prepare(`\n    INSERT INTO memory_fts (text, id, project_id, path, source, tier, start_line, end_line)\n    VALUES (?, ?, ?, ?, ?, ?, ?, ?)\n  `);\n\n  const upsertVaultFile = db.prepare(`\n    INSERT INTO vault_files (vault_path, inode, device, hash, title, indexed_at)\n    VALUES (?, ?, ?, ?, ?, ?)\n    ON CONFLICT(vault_path) DO UPDATE SET\n      inode      = excluded.inode,\n      device     = excluded.device,\n      hash       = excluded.hash,\n      title      = excluded.title,\n      indexed_at = excluded.indexed_at\n  `);\n\n  // ---------------------------------------------------------------------------\n  // Step 4 (cont.): Index each canonical file\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n  let filesSinceYield = 0;\n\n  for (const group of inodeGroups) {\n    // Yield periodically to keep the IPC server responsive\n    if (filesSinceYield >= VAULT_YIELD_EVERY) {\n      await yieldToEventLoop();\n      filesSinceYield = 0;\n    }\n    filesSinceYield++;\n\n    const { canonical } = group;\n\n    // Read file content\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 = selectFileHash.get(canonical.vaultRelPath) as\n      | { hash: string }\n      | undefined;\n\n    if (existing?.hash === hash) {\n      result.filesSkipped++;\n      continue;\n    }\n\n    // Delete old chunks for this vault path\n    const oldChunkIds = deleteOldChunkIds.all(\n      vaultProjectId,\n      canonical.vaultRelPath,\n    ) as Array<{ id: string }>;\n\n    db.transaction(() => {\n      for (const row of oldChunkIds) {\n        deleteFts.run(row.id);\n      }\n      deleteChunks.run(vaultProjectId, canonical.vaultRelPath);\n    })();\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    db.transaction(() => {\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        insertChunk.run(\n          id,\n          vaultProjectId,\n          \"vault\",\n          \"topic\",\n          canonical.vaultRelPath,\n          chunk.startLine,\n          chunk.endLine,\n          chunk.hash,\n          chunk.text,\n          updatedAt,\n        );\n        insertFts.run(\n          chunk.text,\n          id,\n          vaultProjectId,\n          canonical.vaultRelPath,\n          \"vault\",\n          \"topic\",\n          chunk.startLine,\n          chunk.endLine,\n        );\n      }\n      upsertVaultFile.run(\n        canonical.vaultRelPath,\n        canonical.inode,\n        canonical.device,\n        hash,\n        title,\n        updatedAt,\n      );\n    })();\n\n    result.filesIndexed++;\n    result.chunksCreated += chunks.length;\n  }\n\n  // ---------------------------------------------------------------------------\n  // Step 5: Record aliases in vault_aliases\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  // Clear old aliases for this vault before rebuilding\n  // (We identify vault aliases by checking which canonical paths belong to\n  //  the canonical files we just indexed — simpler to clear + rebuild all.)\n  db.exec(\"DELETE FROM vault_aliases\");\n\n  const insertAlias = db.prepare(`\n    INSERT OR REPLACE INTO vault_aliases (vault_path, canonical_path, inode, device)\n    VALUES (?, ?, ?, ?)\n  `);\n\n  const insertAliasesTx = db.transaction((groups: InodeGroup[]) => {\n    for (const group of groups) {\n      for (const alias of group.aliases) {\n        insertAlias.run(\n          alias.vaultRelPath,\n          group.canonical.vaultRelPath,\n          alias.inode,\n          alias.device,\n        );\n        result.aliasesRecorded++;\n      }\n    }\n  });\n  insertAliasesTx(inodeGroups);\n\n  // ---------------------------------------------------------------------------\n  // Step 6: Rebuild vault_name_index\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  db.exec(\"DELETE FROM vault_name_index\");\n\n  const insertNameIndex = db.prepare(`\n    INSERT OR REPLACE INTO vault_name_index (name, vault_path) VALUES (?, ?)\n  `);\n\n  const insertNameIndexTx = db.transaction(\n    (entries: Array<[string, string]>) => {\n      for (const [name, path] of entries) {\n        insertNameIndex.run(name, path);\n      }\n    },\n  );\n\n  const nameEntries: Array<[string, string]> = [];\n  for (const [name, paths] of nameIndex) {\n    for (const path of paths) {\n      nameEntries.push([name, path]);\n    }\n  }\n  insertNameIndexTx(nameEntries);\n\n  // ---------------------------------------------------------------------------\n  // Step 7: Rebuild vault_links\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  db.exec(\"DELETE FROM vault_links\");\n\n  const insertLink = db.prepare(`\n    INSERT OR IGNORE INTO vault_links\n      (source_path, target_raw, target_path, link_type, line_number)\n    VALUES (?, ?, ?, ?, ?)\n  `);\n\n  // Parse and resolve wikilinks in bulk transaction\n  const linkRows: Array<{\n    source: string;\n    raw: string;\n    target: string | null;\n    linkType: string;\n    lineNumber: number;\n  }> = [];\n\n  for (const group of inodeGroups) {\n    const { canonical } = group;\n\n    let content: string;\n    try {\n      content = readFileSync(canonical.absPath, \"utf8\");\n    } catch {\n      continue;\n    }\n\n    const parsedLinks = parseWikilinks(content);\n    for (const link of parsedLinks) {\n      const target = resolveWikilink(link.raw, nameIndex, canonical.vaultRelPath);\n      linkRows.push({\n        source: canonical.vaultRelPath,\n        raw: link.raw,\n        target,\n        linkType: link.isEmbed ? \"embed\" : \"wikilink\",\n        lineNumber: link.lineNumber,\n      });\n    }\n  }\n\n  const insertLinksTx = db.transaction(\n    (\n      rows: Array<{\n        source: string;\n        raw: string;\n        target: string | null;\n        linkType: string;\n        lineNumber: number;\n      }>,\n    ) => {\n      for (const row of rows) {\n        insertLink.run(row.source, row.raw, row.target, row.linkType, row.lineNumber);\n      }\n    },\n  );\n  insertLinksTx(linkRows);\n\n  result.linksExtracted = linkRows.length;\n  result.deadLinksFound = linkRows.filter((r) => r.target === null).length;\n\n  // ---------------------------------------------------------------------------\n  // Step 8: Compute and upsert vault_health metrics\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  // Count outbound links per source\n  const outboundCounts = db\n    .prepare(\n      `SELECT source_path, COUNT(*) AS cnt FROM vault_links GROUP BY source_path`,\n    )\n    .all() as Array<{ source_path: string; cnt: number }>;\n\n  // Count dead links per source\n  const deadLinkCounts = db\n    .prepare(\n      `SELECT source_path, COUNT(*) AS cnt FROM vault_links\n       WHERE target_path IS NULL GROUP BY source_path`,\n    )\n    .all() as Array<{ source_path: string; cnt: number }>;\n\n  // Count inbound links per target\n  const inboundCounts = db\n    .prepare(\n      `SELECT target_path, COUNT(*) AS cnt FROM vault_links\n       WHERE target_path IS NOT NULL GROUP BY target_path`,\n    )\n    .all() as Array<{ target_path: string; cnt: number }>;\n\n  // Build maps for O(1) lookup\n  const outboundMap = new Map<string, number>(\n    outboundCounts.map((r) => [r.source_path, r.cnt]),\n  );\n  const deadMap = new Map<string, number>(\n    deadLinkCounts.map((r) => [r.source_path, r.cnt]),\n  );\n  const inboundMap = new Map<string, number>(\n    inboundCounts.map((r) => [r.target_path, r.cnt]),\n  );\n\n  const upsertHealth = db.prepare(`\n    INSERT INTO vault_health\n      (vault_path, inbound_count, outbound_count, dead_link_count, is_orphan, computed_at)\n    VALUES (?, ?, ?, ?, ?, ?)\n    ON CONFLICT(vault_path) DO UPDATE SET\n      inbound_count   = excluded.inbound_count,\n      outbound_count  = excluded.outbound_count,\n      dead_link_count = excluded.dead_link_count,\n      is_orphan       = excluded.is_orphan,\n      computed_at     = excluded.computed_at\n  `);\n\n  const computedAt = Date.now();\n  let orphanCount = 0;\n\n  const upsertHealthTx = db.transaction((groups: InodeGroup[]) => {\n    for (const group of groups) {\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 ? 1 : 0;\n      if (isOrphan) orphanCount++;\n      upsertHealth.run(path, inbound, outbound, dead, isOrphan, computedAt);\n    }\n  });\n  upsertHealthTx(inodeGroups);\n\n  result.orphansFound = orphanCount;\n  result.elapsed = Date.now() - startTime;\n\n  return 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+{"version":3,"file":"vault-indexer-DXWs9pDn.mjs","names":[],"sources":["../src/memory/vault-indexer.ts"],"sourcesContent":["/**\n * Vault indexer for the PAI federation memory engine.\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.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 { createHash } from \"node:crypto\";\nimport { readFileSync, statSync, readdirSync, existsSync } from \"node:fs\";\nimport { join, relative, basename, dirname, normalize } from \"node:path\";\nimport type { Database } from \"better-sqlite3\";\nimport { chunkMarkdown } from \"./chunker.js\";\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\nexport interface VaultFile {\n  absPath: string;\n  vaultRelPath: string;\n  inode: number;\n  device: number;\n}\n\nexport interface InodeGroup {\n  canonical: VaultFile;\n  aliases: VaultFile[];\n}\n\nexport interface ParsedLink {\n  raw: string;\n  alias: string | null;\n  lineNumber: number;\n  isEmbed: boolean;\n}\n\nexport interface VaultIndexResult {\n  filesIndexed: number;\n  chunksCreated: number;\n  filesSkipped: number;\n  aliasesRecorded: number;\n  linksExtracted: number;\n  deadLinksFound: number;\n  orphansFound: number;\n  elapsed: number;\n}\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\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/** Number of files to process before yielding to the event loop. */\nconst VAULT_YIELD_EVERY = 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// Utility\n// ---------------------------------------------------------------------------\n\nfunction sha256File(content: string): string {\n  return createHash(\"sha256\").update(content).digest(\"hex\");\n}\n\nfunction chunkId(\n  projectId: number,\n  path: string,\n  chunkIndex: number,\n  startLine: number,\n  endLine: number,\n): string {\n  return createHash(\"sha256\")\n    .update(`${projectId}:${path}:${chunkIndex}:${startLine}:${endLine}`)\n    .digest(\"hex\");\n}\n\nfunction yieldToEventLoop(): Promise<void> {\n  return new Promise((resolve) => setImmediate(resolve));\n}\n\n// ---------------------------------------------------------------------------\n// Vault directory walker (follows symlinks)\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 dir        Directory to scan.\n * @param vaultRoot  Absolute root of the vault (for computing vaultRelPath).\n * @param acc        Shared accumulator (mutated in place for early exit).\n * @param visited    Set of \"device:inode\" strings for visited directories.\n * @param depth      Current recursion depth.\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// ---------------------------------------------------------------------------\n// Inode deduplication\n// ---------------------------------------------------------------------------\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// ---------------------------------------------------------------------------\n// Wikilink parser\n// ---------------------------------------------------------------------------\n\n/**\n * Parse all [[wikilinks]] and ![[embeds]] 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 *\n * @param content  Raw markdown file content.\n * @returns        Array of parsed links in document order.\n */\nexport function parseWikilinks(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  for (let lineIdx = 0; lineIdx < lines.length; lineIdx++) {\n    const line = lines[lineIdx]!;\n    const lineNumber = lineIdx + 1; // 1-indexed\n\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      // For frontmatter lines, mark as non-embed regardless of !\n      const isFrontmatter = lineIdx < frontmatterEnd;\n      links.push({\n        raw,\n        alias: alias?.trim() ?? null,\n        lineNumber,\n        isEmbed: isEmbed && !isFrontmatter,\n      });\n    }\n  }\n\n  return links;\n}\n\n// ---------------------------------------------------------------------------\n// Name index builder\n// ---------------------------------------------------------------------------\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// ---------------------------------------------------------------------------\n// Wikilink resolver\n// ---------------------------------------------------------------------------\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  // E.g. \"PAI/20-webseiten/_20-webseiten-master\" → \"_20-webseiten-master\"\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// ---------------------------------------------------------------------------\n// Main vault indexing orchestrator\n// ---------------------------------------------------------------------------\n\n/**\n * Index an entire Obsidian vault (or markdown knowledge base) into the\n * federation database.\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 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 db              Open federation database.\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  db: Database,\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  // ---------------------------------------------------------------------------\n  // Step 1: Walk vault, collecting all .md files (follows symlinks)\n  // ---------------------------------------------------------------------------\n\n  const allFiles = walkVaultMdFiles(vaultRoot);\n\n  // ---------------------------------------------------------------------------\n  // Step 2: Deduplicate by inode\n  // ---------------------------------------------------------------------------\n\n  const inodeGroups = deduplicateByInode(allFiles);\n\n  // ---------------------------------------------------------------------------\n  // Step 3: Build name index (from all files including aliases, for resolution)\n  // ---------------------------------------------------------------------------\n\n  const nameIndex = buildNameIndex(allFiles);\n\n  // ---------------------------------------------------------------------------\n  // Step 4: Prepare SQL statements\n  // ---------------------------------------------------------------------------\n\n  const selectFileHash = db.prepare(\n    \"SELECT hash FROM vault_files WHERE vault_path = ?\",\n  );\n\n  const deleteOldChunkIds = db.prepare(\n    \"SELECT id FROM memory_chunks WHERE project_id = ? AND path = ?\",\n  );\n\n  const deleteFts = db.prepare(\"DELETE FROM memory_fts WHERE id = ?\");\n\n  const deleteChunks = db.prepare(\n    \"DELETE FROM memory_chunks WHERE project_id = ? AND path = ?\",\n  );\n\n  const insertChunk = db.prepare(`\n    INSERT INTO memory_chunks (id, project_id, source, tier, path, start_line, end_line, hash, text, updated_at)\n    VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n  `);\n\n  const insertFts = db.prepare(`\n    INSERT INTO memory_fts (text, id, project_id, path, source, tier, start_line, end_line)\n    VALUES (?, ?, ?, ?, ?, ?, ?, ?)\n  `);\n\n  const upsertVaultFile = db.prepare(`\n    INSERT INTO vault_files (vault_path, inode, device, hash, title, indexed_at)\n    VALUES (?, ?, ?, ?, ?, ?)\n    ON CONFLICT(vault_path) DO UPDATE SET\n      inode      = excluded.inode,\n      device     = excluded.device,\n      hash       = excluded.hash,\n      title      = excluded.title,\n      indexed_at = excluded.indexed_at\n  `);\n\n  // ---------------------------------------------------------------------------\n  // Step 4 (cont.): Index each canonical file\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n  let filesSinceYield = 0;\n\n  for (const group of inodeGroups) {\n    // Yield periodically to keep the IPC server responsive\n    if (filesSinceYield >= VAULT_YIELD_EVERY) {\n      await yieldToEventLoop();\n      filesSinceYield = 0;\n    }\n    filesSinceYield++;\n\n    const { canonical } = group;\n\n    // Read file content\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 = selectFileHash.get(canonical.vaultRelPath) as\n      | { hash: string }\n      | undefined;\n\n    if (existing?.hash === hash) {\n      result.filesSkipped++;\n      continue;\n    }\n\n    // Delete old chunks for this vault path\n    const oldChunkIds = deleteOldChunkIds.all(\n      vaultProjectId,\n      canonical.vaultRelPath,\n    ) as Array<{ id: string }>;\n\n    db.transaction(() => {\n      for (const row of oldChunkIds) {\n        deleteFts.run(row.id);\n      }\n      deleteChunks.run(vaultProjectId, canonical.vaultRelPath);\n    })();\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    db.transaction(() => {\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        insertChunk.run(\n          id,\n          vaultProjectId,\n          \"vault\",\n          \"topic\",\n          canonical.vaultRelPath,\n          chunk.startLine,\n          chunk.endLine,\n          chunk.hash,\n          chunk.text,\n          updatedAt,\n        );\n        insertFts.run(\n          chunk.text,\n          id,\n          vaultProjectId,\n          canonical.vaultRelPath,\n          \"vault\",\n          \"topic\",\n          chunk.startLine,\n          chunk.endLine,\n        );\n      }\n      upsertVaultFile.run(\n        canonical.vaultRelPath,\n        canonical.inode,\n        canonical.device,\n        hash,\n        title,\n        updatedAt,\n      );\n    })();\n\n    result.filesIndexed++;\n    result.chunksCreated += chunks.length;\n  }\n\n  // ---------------------------------------------------------------------------\n  // Step 5: Record aliases in vault_aliases\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  // Clear old aliases for this vault before rebuilding\n  // (We identify vault aliases by checking which canonical paths belong to\n  //  the canonical files we just indexed — simpler to clear + rebuild all.)\n  db.exec(\"DELETE FROM vault_aliases\");\n\n  const insertAlias = db.prepare(`\n    INSERT OR REPLACE INTO vault_aliases (vault_path, canonical_path, inode, device)\n    VALUES (?, ?, ?, ?)\n  `);\n\n  const insertAliasesTx = db.transaction((groups: InodeGroup[]) => {\n    for (const group of groups) {\n      for (const alias of group.aliases) {\n        insertAlias.run(\n          alias.vaultRelPath,\n          group.canonical.vaultRelPath,\n          alias.inode,\n          alias.device,\n        );\n        result.aliasesRecorded++;\n      }\n    }\n  });\n  insertAliasesTx(inodeGroups);\n\n  // ---------------------------------------------------------------------------\n  // Step 6: Rebuild vault_name_index\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  db.exec(\"DELETE FROM vault_name_index\");\n\n  const insertNameIndex = db.prepare(`\n    INSERT OR REPLACE INTO vault_name_index (name, vault_path) VALUES (?, ?)\n  `);\n\n  const insertNameIndexTx = db.transaction(\n    (entries: Array<[string, string]>) => {\n      for (const [name, path] of entries) {\n        insertNameIndex.run(name, path);\n      }\n    },\n  );\n\n  const nameEntries: Array<[string, string]> = [];\n  for (const [name, paths] of nameIndex) {\n    for (const path of paths) {\n      nameEntries.push([name, path]);\n    }\n  }\n  insertNameIndexTx(nameEntries);\n\n  // ---------------------------------------------------------------------------\n  // Step 7: Rebuild vault_links\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  db.exec(\"DELETE FROM vault_links\");\n\n  const insertLink = db.prepare(`\n    INSERT OR IGNORE INTO vault_links\n      (source_path, target_raw, target_path, link_type, line_number)\n    VALUES (?, ?, ?, ?, ?)\n  `);\n\n  // Parse and resolve wikilinks in bulk transaction\n  const linkRows: Array<{\n    source: string;\n    raw: string;\n    target: string | null;\n    linkType: string;\n    lineNumber: number;\n  }> = [];\n\n  for (const group of inodeGroups) {\n    const { canonical } = group;\n\n    let content: string;\n    try {\n      content = readFileSync(canonical.absPath, \"utf8\");\n    } catch {\n      continue;\n    }\n\n    const parsedLinks = parseWikilinks(content);\n    for (const link of parsedLinks) {\n      const target = resolveWikilink(link.raw, nameIndex, canonical.vaultRelPath);\n      linkRows.push({\n        source: canonical.vaultRelPath,\n        raw: link.raw,\n        target,\n        linkType: link.isEmbed ? \"embed\" : \"wikilink\",\n        lineNumber: link.lineNumber,\n      });\n    }\n  }\n\n  const insertLinksTx = db.transaction(\n    (\n      rows: Array<{\n        source: string;\n        raw: string;\n        target: string | null;\n        linkType: string;\n        lineNumber: number;\n      }>,\n    ) => {\n      for (const row of rows) {\n        insertLink.run(row.source, row.raw, row.target, row.linkType, row.lineNumber);\n      }\n    },\n  );\n  insertLinksTx(linkRows);\n\n  result.linksExtracted = linkRows.length;\n  result.deadLinksFound = linkRows.filter((r) => r.target === null).length;\n\n  // ---------------------------------------------------------------------------\n  // Step 8: Compute and upsert vault_health metrics\n  // ---------------------------------------------------------------------------\n\n  await yieldToEventLoop();\n\n  // Count outbound links per source\n  const outboundCounts = db\n    .prepare(\n      `SELECT source_path, COUNT(*) AS cnt FROM vault_links GROUP BY source_path`,\n    )\n    .all() as Array<{ source_path: string; cnt: number }>;\n\n  // Count dead links per source\n  const deadLinkCounts = db\n    .prepare(\n      `SELECT source_path, COUNT(*) AS cnt FROM vault_links\n       WHERE target_path IS NULL GROUP BY source_path`,\n    )\n    .all() as Array<{ source_path: string; cnt: number }>;\n\n  // Count inbound links per target\n  const inboundCounts = db\n    .prepare(\n      `SELECT target_path, COUNT(*) AS cnt FROM vault_links\n       WHERE target_path IS NOT NULL GROUP BY target_path`,\n    )\n    .all() as Array<{ target_path: string; cnt: number }>;\n\n  // Build maps for O(1) lookup\n  const outboundMap = new Map<string, number>(\n    outboundCounts.map((r) => [r.source_path, r.cnt]),\n  );\n  const deadMap = new Map<string, number>(\n    deadLinkCounts.map((r) => [r.source_path, r.cnt]),\n  );\n  const inboundMap = new Map<string, number>(\n    inboundCounts.map((r) => [r.target_path, r.cnt]),\n  );\n\n  const upsertHealth = db.prepare(`\n    INSERT INTO vault_health\n      (vault_path, inbound_count, outbound_count, dead_link_count, is_orphan, computed_at)\n    VALUES (?, ?, ?, ?, ?, ?)\n    ON 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package/dist/{zettelkasten-Co-w0XSZ.mjs → zettelkasten-e-a4rW_6.mjs}

@@ -1,5 +1,5 @@
 import { a as generateEmbedding, n as cosineSimilarity, r as deserializeEmbedding } from "./embeddings-DGRAPAYb.mjs";
-import { i as searchMemoryHybrid } from "./search-GK0ibTJy.mjs";
+import { i as searchMemoryHybrid } from "./search-_oHfguA5.mjs";
 import { basename, dirname } from "node:path";
 
 //#region src/zettelkasten/explore.ts
@@ -898,4 +898,4 @@ async function zettelSuggest(db, opts) {
 
 //#endregion
 export { zettelConverse, zettelExplore, zettelHealth, zettelSuggest, zettelSurprise, zettelThemes };
-//# sourceMappingURL=zettelkasten-Co-w0XSZ.mjs.map
+//# sourceMappingURL=zettelkasten-e-a4rW_6.mjs.map

package/dist/{zettelkasten-Co-w0XSZ.mjs.map → zettelkasten-e-a4rW_6.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"zettelkasten-Co-w0XSZ.mjs","names":["MAX_CHUNKS","MAX_CHUNKS"],"sources":["../src/zettelkasten/explore.ts","../src/zettelkasten/surprise.ts","../src/zettelkasten/converse.ts","../src/zettelkasten/themes.ts","../src/zettelkasten/health.ts","../src/zettelkasten/suggest.ts"],"sourcesContent":["import type { Database } from \"better-sqlite3\";\nimport { dirname } from \"node:path\";\n\nexport interface ExploreOptions {\n  startNote: string;\n  depth?: number;\n  direction?: \"forward\" | \"backward\" | \"both\";\n  mode?: \"sequential\" | \"associative\" | \"all\";\n}\n\nexport interface ExploreNode {\n  path: string;\n  title: string | null;\n  depth: number;\n  linkType: \"sequential\" | \"associative\";\n  inbound: number;\n  outbound: number;\n}\n\nexport interface ExploreResult {\n  root: string;\n  nodes: ExploreNode[];\n  edges: Array<{ from: string; to: string; type: \"sequential\" | \"associative\" }>;\n  branchingPoints: string[];\n  maxDepthReached: boolean;\n}\n\nfunction classifyEdge(source: string, target: string): \"sequential\" | \"associative\" {\n  return dirname(source) === dirname(target) ? \"sequential\" : \"associative\";\n}\n\nfunction resolveStart(db: Database, startNote: string): string | null {\n  const inFiles = db\n    .prepare(\"SELECT vault_path FROM vault_files WHERE vault_path = ?\")\n    .get(startNote) as { vault_path: string } | undefined;\n  if (inFiles) return inFiles.vault_path;\n\n  const alias = db\n    .prepare(\"SELECT canonical_path FROM vault_aliases WHERE vault_path = ?\")\n    .get(startNote) as { canonical_path: string } | undefined;\n  if (!alias) return null;\n\n  const canonical = db\n    .prepare(\"SELECT vault_path FROM vault_files WHERE vault_path = ?\")\n    .get(alias.canonical_path) as { vault_path: string } | undefined;\n  return canonical ? canonical.vault_path : null;\n}\n\nfunction getForwardNeighbors(db: Database, path: string): string[] {\n  return (\n    db\n      .prepare(\n        \"SELECT target_path FROM vault_links WHERE source_path = ? AND target_path IS NOT NULL\",\n      )\n      .all(path) as Array<{ target_path: string }>\n  ).map((r) => r.target_path);\n}\n\nfunction getBackwardNeighbors(db: Database, path: string): string[] {\n  return (\n    db\n      .prepare(\n        \"SELECT source_path FROM vault_links WHERE target_path = ?\",\n      )\n      .all(path) as Array<{ source_path: string }>\n  ).map((r) => r.source_path);\n}\n\nfunction getFileInfo(\n  db: Database,\n  path: string,\n): { title: string | null; inbound: number; outbound: number } {\n  const file = db\n    .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n    .get(path) as { title: string | null } | undefined;\n\n  const health = db\n    .prepare(\"SELECT inbound_count, outbound_count FROM vault_health WHERE vault_path = ?\")\n    .get(path) as { inbound_count: number; outbound_count: number } | undefined;\n\n  return {\n    title: file?.title ?? null,\n    inbound: health?.inbound_count ?? 0,\n    outbound: health?.outbound_count ?? 0,\n  };\n}\n\n/**\n * Traverse the Zettelkasten link graph using BFS, following chains of thought\n * from a starting note up to a configurable depth.\n */\nexport function zettelExplore(db: Database, opts: ExploreOptions): ExploreResult {\n  const depth = Math.min(Math.max(opts.depth ?? 3, 1), 10);\n  const direction = opts.direction ?? \"both\";\n  const mode = opts.mode ?? \"all\";\n\n  const root = resolveStart(db, opts.startNote);\n  if (!root) {\n    return {\n      root: opts.startNote,\n      nodes: [],\n      edges: [],\n      branchingPoints: [],\n      maxDepthReached: false,\n    };\n  }\n\n  const visited = new Set<string>([root]);\n  const nodes: ExploreNode[] = [];\n  const edges: Array<{ from: string; to: string; type: \"sequential\" | \"associative\" }> = [];\n  let maxDepthReached = false;\n\n  const queue: Array<{ path: string; depth: number }> = [{ path: root, depth: 0 }];\n\n  while (queue.length > 0) {\n    const current = queue.shift()!;\n\n    if (current.depth >= depth) {\n      maxDepthReached = true;\n      continue;\n    }\n\n    const neighbors: Array<{ neighbor: string; from: string; to: string }> = [];\n\n    if (direction === \"forward\" || direction === \"both\") {\n      for (const n of getForwardNeighbors(db, current.path)) {\n        neighbors.push({ neighbor: n, from: current.path, to: n });\n      }\n    }\n\n    if (direction === \"backward\" || direction === \"both\") {\n      for (const n of getBackwardNeighbors(db, current.path)) {\n        neighbors.push({ neighbor: n, from: n, to: current.path });\n      }\n    }\n\n    for (const { neighbor, from, to } of neighbors) {\n      const edgeType = classifyEdge(from, to);\n\n      if (mode !== \"all\" && edgeType !== mode) {\n        continue;\n      }\n\n      const edgeKey = `${from}|${to}`;\n      const alreadyHasEdge = edges.some((e) => e.from === from && e.to === to);\n      if (!alreadyHasEdge) {\n        edges.push({ from, to, type: edgeType });\n      }\n\n      if (!visited.has(neighbor)) {\n        visited.add(neighbor);\n\n        const info = getFileInfo(db, neighbor);\n        nodes.push({\n          path: neighbor,\n          title: info.title,\n          depth: current.depth + 1,\n          linkType: edgeType,\n          inbound: info.inbound,\n          outbound: info.outbound,\n        });\n\n        queue.push({ path: neighbor, depth: current.depth + 1 });\n      }\n    }\n  }\n\n  const branchingPoints = nodes\n    .filter((n) => n.outbound > 2)\n    .map((n) => n.path);\n\n  const rootInfo = getFileInfo(db, root);\n  if (rootInfo.outbound > 2) {\n    branchingPoints.unshift(root);\n  }\n\n  return { root, nodes, edges, branchingPoints, maxDepthReached };\n}\n","import type { Database } from \"better-sqlite3\";\nimport {\n  deserializeEmbedding,\n  generateEmbedding,\n  cosineSimilarity,\n} from \"../memory/embeddings.js\";\n\nexport interface SurpriseOptions {\n  referencePath: string;\n  vaultProjectId: number;\n  limit?: number;\n  minSimilarity?: number;\n  minGraphDistance?: number;\n}\n\nexport interface SurpriseResult {\n  path: string;\n  title: string | null;\n  cosineSimilarity: number;\n  graphDistance: number;\n  surpriseScore: number;\n  sharedSnippet: string;\n}\n\nconst CHUNK_BATCH_SIZE = 500;\nconst MAX_CHUNKS = 5000;\nconst BFS_HOP_CAP = 20;\n\nfunction getFileEmbeddings(\n  db: Database,\n  projectId: number,\n): Map<string, { embedding: Float32Array; text: string }> {\n  const rows = db\n    .prepare(\n      `SELECT path, embedding, text FROM memory_chunks\n       WHERE project_id = ? AND embedding IS NOT NULL\n       ORDER BY path, start_line\n       LIMIT ?`,\n    )\n    .all(projectId, MAX_CHUNKS) as Array<{\n    path: string;\n    embedding: Buffer;\n    text: string;\n  }>;\n\n  // Group chunks by path and accumulate embeddings for averaging\n  const byPath = new Map<string, { sum: Float32Array; count: number; text: string }>();\n\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const entry = byPath.get(row.path);\n    if (!entry) {\n      byPath.set(row.path, { sum: new Float32Array(vec), count: 1, text: row.text });\n    } else {\n      for (let i = 0; i < vec.length; i++) {\n        entry.sum[i] += vec[i];\n      }\n      entry.count++;\n    }\n  }\n\n  const result = new Map<string, { embedding: Float32Array; text: string }>();\n  for (const [path, { sum, count, text }] of byPath) {\n    const avg = new Float32Array(sum.length);\n    for (let i = 0; i < sum.length; i++) {\n      avg[i] = sum[i] / count;\n    }\n    result.set(path, { embedding: avg, text });\n  }\n  return result;\n}\n\nfunction getReferenceEmbedding(\n  db: Database,\n  projectId: number,\n  path: string,\n): { embedding: Float32Array; found: boolean } {\n  const rows = db\n    .prepare(\n      `SELECT embedding FROM memory_chunks\n       WHERE project_id = ? AND path = ? AND embedding IS NOT NULL`,\n    )\n    .all(projectId, path) as Array<{ embedding: Buffer }>;\n\n  if (rows.length === 0) {\n    return { embedding: new Float32Array(0), found: false };\n  }\n\n  const dim = deserializeEmbedding(rows[0].embedding).length;\n  const sum = new Float32Array(dim);\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    for (let i = 0; i < dim; i++) {\n      sum[i] += vec[i];\n    }\n  }\n  const avg = new Float32Array(dim);\n  for (let i = 0; i < dim; i++) {\n    avg[i] = sum[i] / rows.length;\n  }\n  return { embedding: avg, found: true };\n}\n\nfunction bfsGraphDistance(db: Database, source: string, target: string): number {\n  if (source === target) return 0;\n\n  const visited = new Set<string>([source]);\n  const queue: Array<{ path: string; hops: number }> = [{ path: source, hops: 0 }];\n\n  while (queue.length > 0) {\n    const { path, hops } = queue.shift()!;\n    if (hops >= BFS_HOP_CAP) continue;\n\n    const neighbors = db\n      .prepare(\n        `SELECT target_path AS neighbor FROM vault_links\n         WHERE source_path = ? AND target_path IS NOT NULL\n         UNION\n         SELECT source_path AS neighbor FROM vault_links\n         WHERE target_path = ?`,\n      )\n      .all(path, path) as Array<{ neighbor: string }>;\n\n    for (const { neighbor } of neighbors) {\n      if (neighbor === target) return hops + 1;\n      if (!visited.has(neighbor)) {\n        visited.add(neighbor);\n        queue.push({ path: neighbor, hops: hops + 1 });\n      }\n    }\n  }\n\n  return Infinity;\n}\n\nfunction getBestChunkText(\n  db: Database,\n  projectId: number,\n  path: string,\n  refEmbedding: Float32Array,\n): string {\n  const rows = db\n    .prepare(\n      `SELECT text, embedding FROM memory_chunks\n       WHERE project_id = ? AND path = ? AND embedding IS NOT NULL\n       LIMIT 20`,\n    )\n    .all(projectId, path) as Array<{ text: string; embedding: Buffer }>;\n\n  if (rows.length === 0) return \"\";\n\n  let bestText = rows[0].text;\n  let bestSim = -Infinity;\n\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const sim = cosineSimilarity(refEmbedding, vec);\n    if (sim > bestSim) {\n      bestSim = sim;\n      bestText = row.text;\n    }\n  }\n\n  return bestText.trim().slice(0, 200);\n}\n\n/**\n * Find notes that are semantically similar to a reference note but graph-distant —\n * revealing surprising conceptual connections across unrelated areas of the Zettelkasten.\n */\nexport async function zettelSurprise(\n  db: Database,\n  opts: SurpriseOptions,\n): Promise<SurpriseResult[]> {\n  const limit = opts.limit ?? 10;\n  const minSimilarity = opts.minSimilarity ?? 0.3;\n  const minGraphDistance = opts.minGraphDistance ?? 3;\n\n  let { embedding: refEmbedding, found } = getReferenceEmbedding(\n    db,\n    opts.vaultProjectId,\n    opts.referencePath,\n  );\n\n  // Fall back to generating an embedding from the file title if no chunks exist\n  if (!found) {\n    const file = db\n      .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n      .get(opts.referencePath) as { title: string | null } | undefined;\n    const text = file?.title ?? opts.referencePath;\n    refEmbedding = await generateEmbedding(text, true);\n  }\n\n  const allFileEmbeddings = getFileEmbeddings(db, opts.vaultProjectId);\n\n  // Remove the reference note itself from candidates\n  allFileEmbeddings.delete(opts.referencePath);\n\n  // First pass: filter by semantic similarity to avoid BFS on all nodes\n  const semanticCandidates: Array<{ path: string; sim: number }> = [];\n  for (const [path, { embedding }] of allFileEmbeddings) {\n    const sim = cosineSimilarity(refEmbedding, embedding);\n    if (sim >= minSimilarity) {\n      semanticCandidates.push({ path, sim });\n    }\n  }\n\n  // Compute graph distances for semantic candidates\n  const results: SurpriseResult[] = [];\n\n  for (const { path, sim } of semanticCandidates) {\n    const graphDistance = bfsGraphDistance(db, opts.referencePath, path);\n\n    const effectiveDistance = isFinite(graphDistance) ? graphDistance : BFS_HOP_CAP;\n    if (effectiveDistance < minGraphDistance) continue;\n\n    const file = db\n      .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n      .get(path) as { title: string | null } | undefined;\n\n    const surpriseScore = sim * Math.log2(effectiveDistance + 1);\n    const sharedSnippet = getBestChunkText(db, opts.vaultProjectId, path, refEmbedding);\n\n    results.push({\n      path,\n      title: file?.title ?? null,\n      cosineSimilarity: sim,\n      graphDistance: isFinite(graphDistance) ? graphDistance : Infinity,\n      surpriseScore,\n      sharedSnippet,\n    });\n  }\n\n  results.sort((a, b) => b.surpriseScore - a.surpriseScore);\n  return results.slice(0, limit);\n}\n","import type { Database } from \"better-sqlite3\";\nimport { searchMemoryHybrid } from \"../memory/search.js\";\nimport { generateEmbedding } from \"../memory/embeddings.js\";\n\nexport interface ConverseOptions {\n  /** The user's question or topic to explore. */\n  question: string;\n  /** project_id for vault chunks in memory_chunks. */\n  vaultProjectId: number;\n  /** Graph expansion depth. Default 2. */\n  depth?: number;\n  /** Maximum number of relevant notes to return. Default 15. */\n  limit?: number;\n}\n\nexport interface ConverseConnection {\n  fromPath: string;\n  toPath: string;\n  /** Top-level folder of fromPath. */\n  fromDomain: string;\n  /** Top-level folder of toPath. */\n  toDomain: string;\n  /** Link count between these two notes (can be > 1). */\n  strength: number;\n}\n\nexport interface ConverseResult {\n  relevantNotes: Array<{\n    path: string;\n    title: string | null;\n    snippet: string;\n    score: number;\n    domain: string;\n  }>;\n  /** Cross-domain connections found among the selected notes. */\n  connections: ConverseConnection[];\n  /** Unique domains involved across all selected notes. */\n  domains: string[];\n  /** AI-ready prompt combining notes + connections for insight generation. */\n  synthesisPrompt: string;\n}\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Extract the top-level folder from a vault path (first path segment). */\nfunction extractDomain(vaultPath: string): string {\n  const slash = vaultPath.indexOf(\"/\");\n  return slash === -1 ? vaultPath : vaultPath.slice(0, slash);\n}\n\n/**\n * Expand one level of graph neighbors for a set of paths.\n * Returns all outbound and inbound neighbor paths (excluding already-visited).\n */\nfunction expandNeighbors(db: Database, paths: Set<string>): string[] {\n  if (paths.size === 0) return [];\n\n  const placeholders = Array.from(paths).map(() => \"?\").join(\", \");\n  const pathList = Array.from(paths);\n\n  const forward = db\n    .prepare(\n      `SELECT DISTINCT target_path FROM vault_links WHERE source_path IN (${placeholders}) AND target_path IS NOT NULL`,\n    )\n    .all(...pathList) as Array<{ target_path: string }>;\n\n  const backward = db\n    .prepare(\n      `SELECT DISTINCT source_path FROM vault_links WHERE target_path IN (${placeholders})`,\n    )\n    .all(...pathList) as Array<{ source_path: string }>;\n\n  const neighbors: string[] = [];\n  for (const r of forward) neighbors.push(r.target_path);\n  for (const r of backward) neighbors.push(r.source_path);\n  return neighbors;\n}\n\n/**\n * Look up the title for a single vault path.\n * Returns null when the path is not found in vault_files.\n */\nfunction getTitle(db: Database, path: string): string | null {\n  const row = db\n    .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n    .get(path) as { title: string | null } | undefined;\n  return row?.title ?? null;\n}\n\n/**\n * Count inbound links for a path from vault_health.\n * Used as a tiebreaker when trimming neighbor-only notes.\n */\nfunction getInboundCount(db: Database, path: string): number {\n  const row = db\n    .prepare(\"SELECT inbound_count FROM vault_health WHERE vault_path = ?\")\n    .get(path) as { inbound_count: number } | undefined;\n  return row?.inbound_count ?? 0;\n}\n\n// ---------------------------------------------------------------------------\n// Main export\n// ---------------------------------------------------------------------------\n\n/**\n * Let the vault \"talk back\" — find notes relevant to a question, expand\n * through the link graph, identify cross-domain connections, and return a\n * structured result including a synthesis prompt for an AI to generate insights.\n */\nexport async function zettelConverse(\n  db: Database,\n  opts: ConverseOptions,\n): Promise<ConverseResult> {\n  const depth = Math.max(opts.depth ?? 2, 0);\n  const limit = Math.max(opts.limit ?? 15, 1);\n  const candidateLimit = 20;\n\n  // ------------------------------------------------------------------\n  // 1. Hybrid search: find top candidates via BM25 + semantic similarity\n  // ------------------------------------------------------------------\n  const queryEmbedding = await generateEmbedding(opts.question, true);\n\n  const searchResults = searchMemoryHybrid(\n    db,\n    opts.question,\n    queryEmbedding,\n    {\n      projectIds: [opts.vaultProjectId],\n      maxResults: candidateLimit,\n    },\n  );\n\n  // Map of path -> best score + snippet from search results\n  const searchHits = new Map<string, { score: number; snippet: string }>();\n  for (const r of searchResults) {\n    const existing = searchHits.get(r.path);\n    if (!existing || r.score > existing.score) {\n      searchHits.set(r.path, { score: r.score, snippet: r.snippet });\n    }\n  }\n\n  // ------------------------------------------------------------------\n  // 2. Graph expansion: BFS from each search result up to `depth` levels\n  // ------------------------------------------------------------------\n  const allPaths = new Set<string>(searchHits.keys());\n  let frontier = new Set<string>(searchHits.keys());\n\n  for (let d = 0; d < depth; d++) {\n    const neighbors = expandNeighbors(db, frontier);\n    const newFrontier = new Set<string>();\n    for (const n of neighbors) {\n      if (!allPaths.has(n)) {\n        allPaths.add(n);\n        newFrontier.add(n);\n      }\n    }\n    if (newFrontier.size === 0) break;\n    frontier = newFrontier;\n  }\n\n  // ------------------------------------------------------------------\n  // 3. Deduplicate + trim to limit\n  //    Search results first (ranked by score), then neighbors by inbound count\n  // ------------------------------------------------------------------\n  const searchRanked = Array.from(searchHits.entries())\n    .sort((a, b) => b[1].score - a[1].score)\n    .map(([path, info]) => ({ path, ...info, isSearchResult: true }));\n\n  const neighborPaths = Array.from(allPaths).filter((p) => !searchHits.has(p));\n\n  // Sort neighbors by link popularity (inbound count) so that well-connected\n  // notes are preferred when we have budget for them.\n  const neighborRanked = neighborPaths\n    .map((path) => ({\n      path,\n      score: 0,\n      snippet: \"\",\n      inbound: getInboundCount(db, path),\n      isSearchResult: false,\n    }))\n    .sort((a, b) => b.inbound - a.inbound);\n\n  // Combine: search results fill the budget first, then neighbors\n  const budgetForNeighbors = Math.max(limit - searchRanked.length, 0);\n  const selectedNeighbors = neighborRanked.slice(0, budgetForNeighbors);\n\n  const selectedSearchPaths = searchRanked.slice(0, limit);\n  const selectedPaths = new Set<string>([\n    ...selectedSearchPaths.map((r) => r.path),\n    ...selectedNeighbors.map((r) => r.path),\n  ]);\n\n  // ------------------------------------------------------------------\n  // 4. Build relevantNotes with titles + domains\n  // ------------------------------------------------------------------\n  const relevantNotes: ConverseResult[\"relevantNotes\"] = [];\n\n  for (const r of selectedSearchPaths) {\n    if (!selectedPaths.has(r.path)) continue;\n    relevantNotes.push({\n      path: r.path,\n      title: getTitle(db, r.path),\n      snippet: r.snippet,\n      score: r.score,\n      domain: extractDomain(r.path),\n    });\n  }\n\n  for (const r of selectedNeighbors) {\n    relevantNotes.push({\n      path: r.path,\n      title: getTitle(db, r.path),\n      snippet: r.snippet,\n      score: 0,\n      domain: extractDomain(r.path),\n    });\n  }\n\n  // ------------------------------------------------------------------\n  // 5. Find connections between the selected notes\n  // ------------------------------------------------------------------\n  let connections: ConverseConnection[] = [];\n\n  if (selectedPaths.size > 0) {\n    const pathList = Array.from(selectedPaths);\n    const placeholders = pathList.map(() => \"?\").join(\", \");\n\n    const edgeRows = db\n      .prepare(\n        `SELECT source_path, target_path, COUNT(*) AS cnt\n         FROM vault_links\n         WHERE source_path IN (${placeholders})\n           AND target_path IN (${placeholders})\n         GROUP BY source_path, target_path`,\n      )\n      .all(...pathList, ...pathList) as Array<{\n        source_path: string;\n        target_path: string;\n        cnt: number;\n      }>;\n\n    for (const row of edgeRows) {\n      connections.push({\n        fromPath: row.source_path,\n        toPath: row.target_path,\n        fromDomain: extractDomain(row.source_path),\n        toDomain: extractDomain(row.target_path),\n        strength: row.cnt,\n      });\n    }\n  }\n\n  // ------------------------------------------------------------------\n  // 6. Domains + cross-domain filter\n  // ------------------------------------------------------------------\n  const domainSet = new Set<string>(relevantNotes.map((n) => n.domain));\n  const domains = Array.from(domainSet).sort();\n\n  const crossDomainConnections = connections.filter(\n    (c) => c.fromDomain !== c.toDomain,\n  );\n\n  // ------------------------------------------------------------------\n  // 7. Build synthesis prompt\n  // ------------------------------------------------------------------\n  const notesSummary = relevantNotes\n    .map((n, i) => {\n      const title = n.title ? `\"${n.title}\"` : \"(untitled)\";\n      const domain = n.domain;\n      const scoreLabel = n.score > 0 ? ` [relevance: ${n.score.toFixed(3)}]` : \" [context]\";\n      const snippet = n.snippet.trim().slice(0, 300);\n      return `${i + 1}. [${domain}] ${title}${scoreLabel}\\n   Path: ${n.path}\\n   \"${snippet}\"`;\n    })\n    .join(\"\\n\\n\");\n\n  const connectionSummary =\n    crossDomainConnections.length > 0\n      ? crossDomainConnections\n          .map(\n            (c) =>\n              `- \"${c.fromPath}\" (${c.fromDomain}) → \"${c.toPath}\" (${c.toDomain}) [strength: ${c.strength}]`,\n          )\n          .join(\"\\n\")\n      : \"(no cross-domain connections found)\";\n\n  const domainList = domains.join(\", \");\n\n  const synthesisPrompt = `You are a Zettelkasten research assistant. The vault has surfaced the following notes in response to this question:\n\nQUESTION: ${opts.question}\n\n---\n\nRELEVANT NOTES (${relevantNotes.length} notes across ${domains.length} domain(s): ${domainList}):\n\n${notesSummary}\n\n---\n\nCROSS-DOMAIN CONNECTIONS (links bridging different knowledge areas):\n\n${connectionSummary}\n\n---\n\nSYNTHESIS TASK:\n\nBased on these notes and the connections between them, please:\n\n1. Identify the key insights that emerge in direct response to the question.\n2. Highlight any unexpected connections between notes from different domains (${domainList}).\n3. Point out tensions, contradictions, or open questions the vault raises but does not resolve.\n4. Suggest what is notably absent — what the vault does NOT yet contain that would strengthen the understanding of this topic.\n5. Propose 2-3 new notes that would meaningfully extend this knowledge cluster.\n\nThink like a scholar who has deeply internalized these ideas and is now synthesizing them for the first time.`;\n\n  return {\n    relevantNotes,\n    connections: crossDomainConnections,\n    domains,\n    synthesisPrompt,\n  };\n}\n","import type { Database } from \"better-sqlite3\";\nimport { deserializeEmbedding, cosineSimilarity } from \"../memory/embeddings.js\";\n\nexport interface ThemeOptions {\n  vaultProjectId: number;\n  lookbackDays?: number;\n  minClusterSize?: number;\n  maxThemes?: number;\n  similarityThreshold?: number;\n}\n\nexport interface ThemeCluster {\n  id: number;\n  label: string;\n  notes: Array<{\n    path: string;\n    title: string | null;\n  }>;\n  size: number;\n  folderDiversity: number;\n  avgRecency: number;\n  linkedRatio: number;\n  suggestIndexNote: boolean;\n}\n\nexport interface ThemeResult {\n  themes: ThemeCluster[];\n  totalNotesAnalyzed: number;\n  timeWindow: { from: number; to: number };\n}\n\nconst MAX_CHUNKS = 5000;\n\nconst STOP_WORDS = new Set([\n  \"a\", \"an\", \"the\", \"and\", \"or\", \"but\", \"in\", \"on\", \"at\", \"to\", \"for\",\n  \"of\", \"with\", \"by\", \"from\", \"is\", \"it\", \"as\", \"be\", \"was\", \"are\",\n  \"has\", \"had\", \"have\", \"not\", \"this\", \"that\", \"i\", \"my\", \"we\", \"our\",\n  \"new\", \"note\", \"untitled\", \"page\", \"file\", \"doc\",\n]);\n\nfunction getTopFolder(vaultPath: string): string {\n  const parts = vaultPath.split(\"/\");\n  return parts.length > 1 ? parts[0] : \"\";\n}\n\nfunction generateLabel(titles: Array<string | null>): string {\n  const wordCounts = new Map<string, number>();\n  for (const title of titles) {\n    if (!title) continue;\n    const words = title\n      .toLowerCase()\n      .replace(/[^a-z0-9\\s]/g, \" \")\n      .split(/\\s+/)\n      .filter((w) => w.length > 2 && !STOP_WORDS.has(w));\n    for (const word of words) {\n      wordCounts.set(word, (wordCounts.get(word) ?? 0) + 1);\n    }\n  }\n  const sorted = [...wordCounts.entries()].sort((a, b) => b[1] - a[1]);\n  return sorted\n    .slice(0, 3)\n    .map(([w]) => w)\n    .join(\" / \");\n}\n\nfunction computeLinkedRatio(db: Database, paths: string[]): number {\n  if (paths.length < 2) return 0;\n  const totalPairs = (paths.length * (paths.length - 1)) / 2;\n  const pathSet = new Set(paths);\n  let linkedPairs = 0;\n\n  for (const path of paths) {\n    const rows = db\n      .prepare(\n        `SELECT target_path FROM vault_links\n         WHERE source_path = ? AND target_path IS NOT NULL`,\n      )\n      .all(path) as Array<{ target_path: string }>;\n    for (const { target_path } of rows) {\n      if (pathSet.has(target_path)) {\n        linkedPairs++;\n      }\n    }\n  }\n\n  // Each bidirectional pair might be counted once per direction; divide by 2 to normalize\n  const uniquePairs = linkedPairs / 2;\n  return Math.min(1, uniquePairs / totalPairs);\n}\n\ntype ClusterNode = {\n  paths: string[];\n  titles: Array<string | null>;\n  indexedAts: number[];\n  centroid: Float32Array;\n};\n\nfunction averageEmbeddings(embeddings: Float32Array[]): Float32Array {\n  if (embeddings.length === 0) return new Float32Array(0);\n  const dim = embeddings[0].length;\n  const sum = new Float32Array(dim);\n  for (const vec of embeddings) {\n    for (let i = 0; i < dim; i++) {\n      sum[i] += vec[i];\n    }\n  }\n  const avg = new Float32Array(dim);\n  for (let i = 0; i < dim; i++) {\n    avg[i] = sum[i] / embeddings.length;\n  }\n  return avg;\n}\n\n/**\n * Detect emerging themes in recently-modified notes using agglomerative single-linkage\n * clustering of note-level embeddings.\n */\nexport async function zettelThemes(\n  db: Database,\n  opts: ThemeOptions,\n): Promise<ThemeResult> {\n  const lookbackDays = opts.lookbackDays ?? 30;\n  const minClusterSize = opts.minClusterSize ?? 3;\n  const maxThemes = opts.maxThemes ?? 10;\n  const similarityThreshold = opts.similarityThreshold ?? 0.65;\n\n  const now = Date.now();\n  const from = now - lookbackDays * 86400000;\n\n  // Step 1: get recent notes\n  const recentNotes = db\n    .prepare(\n      `SELECT vault_path, title, indexed_at FROM vault_files WHERE indexed_at > ?`,\n    )\n    .all(from) as Array<{ vault_path: string; title: string | null; indexed_at: number }>;\n\n  // Step 2: get file-level embeddings from memory_chunks\n  const chunkRows = db\n    .prepare(\n      `SELECT path, embedding FROM memory_chunks\n       WHERE project_id = ? AND embedding IS NOT NULL\n       ORDER BY path, start_line\n       LIMIT ?`,\n    )\n    .all(opts.vaultProjectId, MAX_CHUNKS) as Array<{ path: string; embedding: Buffer }>;\n\n  const embeddingsByPath = new Map<string, Float32Array[]>();\n  for (const row of chunkRows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const arr = embeddingsByPath.get(row.path);\n    if (!arr) {\n      embeddingsByPath.set(row.path, [vec]);\n    } else {\n      arr.push(vec);\n    }\n  }\n\n  const fileEmbeddings = new Map<string, Float32Array>();\n  for (const [path, vecs] of embeddingsByPath) {\n    fileEmbeddings.set(path, averageEmbeddings(vecs));\n  }\n\n  // Step 3: build initial clusters — only include notes that have embeddings\n  const clusters: ClusterNode[] = [];\n  for (const note of recentNotes) {\n    const embedding = fileEmbeddings.get(note.vault_path);\n    if (!embedding) continue;\n    clusters.push({\n      paths: [note.vault_path],\n      titles: [note.title],\n      indexedAts: [note.indexed_at],\n      centroid: embedding,\n    });\n  }\n\n  const totalNotesAnalyzed = clusters.length;\n\n  // Step 4: agglomerative single-linkage clustering\n  // Stop when no two clusters have similarity >= threshold\n  // Using centroid similarity as a proxy for single-linkage max similarity\n  let merged = true;\n  while (merged && clusters.length > 1) {\n    merged = false;\n    let bestSim = similarityThreshold;\n    let bestI = -1;\n    let bestJ = -1;\n\n    for (let i = 0; i < clusters.length; i++) {\n      for (let j = i + 1; j < clusters.length; j++) {\n        const sim = cosineSimilarity(clusters[i].centroid, clusters[j].centroid);\n        if (sim > bestSim) {\n          bestSim = sim;\n          bestI = i;\n          bestJ = j;\n        }\n      }\n    }\n\n    if (bestI === -1) break;\n\n    // Merge cluster j into cluster i\n    const ci = clusters[bestI];\n    const cj = clusters[bestJ];\n    const mergedPaths = [...ci.paths, ...cj.paths];\n    const mergedTitles = [...ci.titles, ...cj.titles];\n    const mergedIndexedAts = [...ci.indexedAts, ...cj.indexedAts];\n\n    // Recompute centroid from averaged embeddings of all member paths\n    const memberEmbeddings: Float32Array[] = [];\n    for (const p of mergedPaths) {\n      const emb = fileEmbeddings.get(p);\n      if (emb) memberEmbeddings.push(emb);\n    }\n\n    clusters[bestI] = {\n      paths: mergedPaths,\n      titles: mergedTitles,\n      indexedAts: mergedIndexedAts,\n      centroid: averageEmbeddings(memberEmbeddings),\n    };\n\n    clusters.splice(bestJ, 1);\n    merged = true;\n  }\n\n  // Step 5: filter and annotate clusters\n  const themes: ThemeCluster[] = [];\n  let clusterIndex = 0;\n\n  for (const cluster of clusters) {\n    if (cluster.paths.length < minClusterSize) continue;\n\n    const label = generateLabel(cluster.titles) || `Theme ${clusterIndex + 1}`;\n    const avgRecency =\n      cluster.indexedAts.reduce((sum, t) => sum + t, 0) / cluster.indexedAts.length;\n\n    const uniqueFolders = new Set(cluster.paths.map(getTopFolder));\n    const folderDiversity = uniqueFolders.size / cluster.paths.length;\n\n    const linkedRatio = computeLinkedRatio(db, cluster.paths);\n    const suggestIndexNote = linkedRatio < 0.3 && cluster.paths.length >= 5;\n\n    themes.push({\n      id: clusterIndex++,\n      label,\n      notes: cluster.paths.map((path, idx) => ({\n        path,\n        title: cluster.titles[idx],\n      })),\n      size: cluster.paths.length,\n      folderDiversity,\n      avgRecency,\n      linkedRatio,\n      suggestIndexNote,\n    });\n  }\n\n  // Step 6: rank by size * folderDiversity * recency_ratio\n  themes.sort(\n    (a, b) =>\n      b.size * b.folderDiversity * (b.avgRecency / now) -\n      a.size * a.folderDiversity * (a.avgRecency / now),\n  );\n\n  return {\n    themes: themes.slice(0, maxThemes),\n    totalNotesAnalyzed,\n    timeWindow: { from, to: now },\n  };\n}\n","import type { Database } from \"better-sqlite3\";\n\nexport interface HealthOptions {\n  scope?: \"full\" | \"recent\" | \"project\";\n  projectPath?: string;\n  recentDays?: number;\n  include?: Array<\"dead_links\" | \"orphans\" | \"disconnected\" | \"low_connectivity\">;\n}\n\nexport interface DeadLink {\n  sourcePath: string;\n  targetRaw: string;\n  lineNumber: number;\n}\n\nexport interface HealthResult {\n  totalFiles: number;\n  totalLinks: number;\n  deadLinks: DeadLink[];\n  orphans: string[];\n  disconnectedClusters: number;\n  lowConnectivity: string[];\n  healthScore: number;\n  computedAt: number;\n}\n\nfunction buildScopeFilter(\n  opts: HealthOptions,\n  tableAlias: string,\n  pathColumn: string,\n): { clause: string; params: unknown[] } {\n  const scope = opts.scope ?? \"full\";\n\n  if (scope === \"project\") {\n    const prefix = opts.projectPath ?? \"\";\n    return {\n      clause: `WHERE ${tableAlias}.${pathColumn} LIKE ? || '%'`,\n      params: [prefix],\n    };\n  }\n\n  if (scope === \"recent\") {\n    const days = opts.recentDays ?? 30;\n    const cutoff = Date.now() - days * 86400000;\n    return {\n      clause: `WHERE ${tableAlias}.indexed_at > ?`,\n      params: [cutoff],\n    };\n  }\n\n  return { clause: \"\", params: [] };\n}\n\nfunction countComponents(nodes: string[], edges: Array<{ source: string; target: string }>): number {\n  if (nodes.length === 0) return 0;\n\n  const parent = new Map<string, string>();\n  const rank = new Map<string, number>();\n\n  for (const n of nodes) {\n    parent.set(n, n);\n    rank.set(n, 0);\n  }\n\n  function find(x: string): string {\n    let root = x;\n    while (parent.get(root) !== root) {\n      root = parent.get(root)!;\n    }\n    let current = x;\n    while (current !== root) {\n      const next = parent.get(current)!;\n      parent.set(current, root);\n      current = next;\n    }\n    return root;\n  }\n\n  function union(a: string, b: string): void {\n    const ra = find(a);\n    const rb = find(b);\n    if (ra === rb) return;\n    const rankA = rank.get(ra) ?? 0;\n    const rankB = rank.get(rb) ?? 0;\n    if (rankA < rankB) {\n      parent.set(ra, rb);\n    } else if (rankA > rankB) {\n      parent.set(rb, ra);\n    } else {\n      parent.set(rb, ra);\n      rank.set(ra, rankA + 1);\n    }\n  }\n\n  for (const { source, target } of edges) {\n    if (parent.has(source) && parent.has(target)) {\n      union(source, target);\n    }\n  }\n\n  const roots = new Set<string>();\n  for (const n of nodes) {\n    roots.add(find(n));\n  }\n  return roots.size;\n}\n\n/**\n * Audit the structural health of the Zettelkasten vault using graph metrics.\n * Designed to complete in under 60ms for a full vault.\n */\nexport function zettelHealth(db: Database, opts?: HealthOptions): HealthResult {\n  const options = opts ?? {};\n  const scope = options.scope ?? \"full\";\n  const include = options.include ?? [\"dead_links\", \"orphans\", \"disconnected\", \"low_connectivity\"];\n\n  const computedAt = Date.now();\n\n  // --- totalFiles ---\n  let totalFiles = 0;\n  if (scope === \"full\") {\n    totalFiles = (\n      db.prepare(\"SELECT COUNT(*) AS n FROM vault_files\").get() as { n: number }\n    ).n;\n  } else if (scope === \"project\") {\n    const prefix = options.projectPath ?? \"\";\n    totalFiles = (\n      db\n        .prepare(\"SELECT COUNT(*) AS n FROM vault_files WHERE vault_path LIKE ? || '%'\")\n        .get(prefix) as { n: number }\n    ).n;\n  } else {\n    const days = options.recentDays ?? 30;\n    const cutoff = computedAt - days * 86400000;\n    totalFiles = (\n      db\n        .prepare(\"SELECT COUNT(*) AS n FROM vault_files WHERE indexed_at > ?\")\n        .get(cutoff) as { n: number }\n    ).n;\n  }\n\n  // --- totalLinks ---\n  let totalLinks = 0;\n  if (scope === \"full\") {\n    totalLinks = (\n      db.prepare(\"SELECT COUNT(*) AS n FROM vault_links\").get() as { n: number }\n    ).n;\n  } else if (scope === \"project\") {\n    const prefix = options.projectPath ?? \"\";\n    totalLinks = (\n      db\n        .prepare(\"SELECT COUNT(*) AS n FROM vault_links WHERE source_path LIKE ? || '%'\")\n        .get(prefix) as { n: number }\n    ).n;\n  } else {\n    const days = options.recentDays ?? 30;\n    const cutoff = computedAt - days * 86400000;\n    totalLinks = (\n      db\n        .prepare(\n          \"SELECT COUNT(*) AS n FROM vault_links WHERE source_path IN (SELECT vault_path FROM vault_files WHERE indexed_at > ?)\",\n        )\n        .get(cutoff) as { n: number }\n    ).n;\n  }\n\n  // --- deadLinks ---\n  let deadLinks: DeadLink[] = [];\n  if (include.includes(\"dead_links\")) {\n    if (scope === \"full\") {\n      deadLinks = (\n        db\n          .prepare(\n            \"SELECT source_path, target_raw, line_number FROM vault_links WHERE target_path IS NULL\",\n          )\n          .all() as Array<{ source_path: string; target_raw: string; line_number: number }>\n      ).map((r) => ({\n        sourcePath: r.source_path,\n        targetRaw: r.target_raw,\n        lineNumber: r.line_number,\n      }));\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      deadLinks = (\n        db\n          .prepare(\n            \"SELECT source_path, target_raw, line_number FROM vault_links WHERE target_path IS NULL AND source_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ source_path: string; target_raw: string; line_number: number }>\n      ).map((r) => ({\n        sourcePath: r.source_path,\n        targetRaw: r.target_raw,\n        lineNumber: r.line_number,\n      }));\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      deadLinks = (\n        db\n          .prepare(\n            \"SELECT source_path, target_raw, line_number FROM vault_links WHERE target_path IS NULL AND source_path IN (SELECT vault_path FROM vault_files WHERE indexed_at > ?)\",\n          )\n          .all(cutoff) as Array<{ source_path: string; target_raw: string; line_number: number }>\n      ).map((r) => ({\n        sourcePath: r.source_path,\n        targetRaw: r.target_raw,\n        lineNumber: r.line_number,\n      }));\n    }\n  }\n\n  // --- orphans ---\n  let orphans: string[] = [];\n  if (include.includes(\"orphans\")) {\n    if (scope === \"full\") {\n      orphans = (\n        db\n          .prepare(\"SELECT vault_path FROM vault_health WHERE is_orphan = 1\")\n          .all() as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      orphans = (\n        db\n          .prepare(\n            \"SELECT vault_path FROM vault_health WHERE is_orphan = 1 AND vault_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      orphans = (\n        db\n          .prepare(\n            \"SELECT vh.vault_path FROM vault_health vh JOIN vault_files vf ON vh.vault_path = vf.vault_path WHERE vh.is_orphan = 1 AND vf.indexed_at > ?\",\n          )\n          .all(cutoff) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    }\n  }\n\n  // --- disconnectedClusters (union-find) ---\n  let disconnectedClusters = 1;\n  if (include.includes(\"disconnected\")) {\n    let allNodes: string[];\n    let allEdges: Array<{ source: string; target: string }>;\n\n    if (scope === \"full\") {\n      allNodes = (\n        db.prepare(\"SELECT vault_path FROM vault_files\").all() as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n\n      allEdges = (\n        db\n          .prepare(\n            \"SELECT DISTINCT source_path AS source, target_path AS target FROM vault_links WHERE target_path IS NOT NULL\",\n          )\n          .all() as Array<{ source: string; target: string }>\n      );\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      allNodes = (\n        db\n          .prepare(\"SELECT vault_path FROM vault_files WHERE vault_path LIKE ? || '%'\")\n          .all(prefix) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n\n      allEdges = (\n        db\n          .prepare(\n            \"SELECT DISTINCT source_path AS source, target_path AS target FROM vault_links WHERE target_path IS NOT NULL AND source_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ source: string; target: string }>\n      );\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      allNodes = (\n        db\n          .prepare(\"SELECT vault_path FROM vault_files WHERE indexed_at > ?\")\n          .all(cutoff) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n\n      allEdges = (\n        db\n          .prepare(\n            \"SELECT DISTINCT source_path AS source, target_path AS target FROM vault_links WHERE target_path IS NOT NULL AND source_path IN (SELECT vault_path FROM vault_files WHERE indexed_at > ?)\",\n          )\n          .all(cutoff) as Array<{ source: string; target: string }>\n      );\n    }\n\n    disconnectedClusters = countComponents(allNodes, allEdges);\n  }\n\n  // --- lowConnectivity ---\n  let lowConnectivity: string[] = [];\n  if (include.includes(\"low_connectivity\")) {\n    if (scope === \"full\") {\n      lowConnectivity = (\n        db\n          .prepare(\n            \"SELECT vault_path FROM vault_health WHERE inbound_count + outbound_count <= 1\",\n          )\n          .all() as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      lowConnectivity = (\n        db\n          .prepare(\n            \"SELECT vault_path FROM vault_health WHERE inbound_count + outbound_count <= 1 AND vault_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      lowConnectivity = (\n        db\n          .prepare(\n            \"SELECT vh.vault_path FROM vault_health vh JOIN vault_files vf ON vh.vault_path = vf.vault_path WHERE vh.inbound_count + vh.outbound_count <= 1 AND vf.indexed_at > ?\",\n          )\n          .all(cutoff) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    }\n  }\n\n  // --- healthScore ---\n  const deadRatio = totalLinks > 0 ? deadLinks.length / totalLinks : 0;\n  const orphanRatio = totalFiles > 0 ? orphans.length / totalFiles : 0;\n  const lowConnRatio = totalFiles > 0 ? lowConnectivity.length / totalFiles : 0;\n  const healthScore = Math.round(\n    100 * (1 - deadRatio) * (1 - orphanRatio * 0.5) * (1 - lowConnRatio * 0.3),\n  );\n\n  return {\n    totalFiles,\n    totalLinks,\n    deadLinks,\n    orphans,\n    disconnectedClusters,\n    lowConnectivity,\n    healthScore,\n    computedAt,\n  };\n}\n","import type { Database } from \"better-sqlite3\";\nimport { deserializeEmbedding, cosineSimilarity } from \"../memory/embeddings.js\";\nimport { basename } from \"node:path\";\n\nexport interface SuggestOptions {\n  notePath: string;\n  vaultProjectId: number;\n  limit?: number;\n  excludeLinked?: boolean;\n}\n\nexport interface Suggestion {\n  path: string;\n  title: string | null;\n  score: number;\n  semanticScore: number;\n  tagScore: number;\n  neighborScore: number;\n  reason: string;\n  suggestedWikilink: string;\n}\n\nconst MAX_CHUNKS = 5000;\nconst SEMANTIC_WEIGHT = 0.5;\nconst TAG_WEIGHT = 0.2;\nconst NEIGHBOR_WEIGHT = 0.3;\n\n// Stop words to ignore when generating tag/label strings\nconst STOP_WORDS = new Set([\n  \"a\", \"an\", \"the\", \"and\", \"or\", \"but\", \"in\", \"on\", \"at\", \"to\", \"for\",\n  \"of\", \"with\", \"by\", \"from\", \"is\", \"it\", \"as\", \"be\", \"was\", \"are\",\n  \"has\", \"had\", \"have\", \"not\", \"this\", \"that\", \"i\", \"my\", \"we\", \"our\",\n]);\n\nfunction extractTagsFromChunkTexts(texts: string[]): Set<string> {\n  const tags = new Set<string>();\n  for (const text of texts) {\n    // Match YAML frontmatter tags block: \"tags:\\n  - tag1\\n  - tag2\"\n    const match = text.match(/^tags:\\s*\\n((?:[ \\t]*-[ \\t]*.+\\n?)*)/m);\n    if (!match) continue;\n    const block = match[1];\n    const lines = block.split(\"\\n\");\n    for (const line of lines) {\n      const tagMatch = line.match(/^[ \\t]*-[ \\t]*(.+)/);\n      if (tagMatch) {\n        const tag = tagMatch[1].trim().toLowerCase();\n        if (tag) tags.add(tag);\n      }\n    }\n  }\n  return tags;\n}\n\nfunction getFileAvgEmbedding(\n  db: Database,\n  projectId: number,\n  path: string,\n): Float32Array | null {\n  const rows = db\n    .prepare(\n      `SELECT embedding FROM memory_chunks\n       WHERE project_id = ? AND path = ? AND embedding IS NOT NULL`,\n    )\n    .all(projectId, path) as Array<{ embedding: Buffer }>;\n\n  if (rows.length === 0) return null;\n\n  const first = deserializeEmbedding(rows[0].embedding);\n  const sum = new Float32Array(first.length);\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    for (let i = 0; i < vec.length; i++) {\n      sum[i] += vec[i];\n    }\n  }\n  const avg = new Float32Array(sum.length);\n  for (let i = 0; i < sum.length; i++) {\n    avg[i] = sum[i] / rows.length;\n  }\n  return avg;\n}\n\nfunction getAllFileEmbeddings(\n  db: Database,\n  projectId: number,\n): Map<string, Float32Array> {\n  const rows = db\n    .prepare(\n      `SELECT path, embedding FROM memory_chunks\n       WHERE project_id = ? AND embedding IS NOT NULL\n       ORDER BY path, start_line\n       LIMIT ?`,\n    )\n    .all(projectId, MAX_CHUNKS) as Array<{ path: string; embedding: Buffer }>;\n\n  const byPath = new Map<string, { sum: Float32Array; count: number }>();\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const entry = byPath.get(row.path);\n    if (!entry) {\n      byPath.set(row.path, { sum: new Float32Array(vec), count: 1 });\n    } else {\n      for (let i = 0; i < vec.length; i++) {\n        entry.sum[i] += vec[i];\n      }\n      entry.count++;\n    }\n  }\n\n  const result = new Map<string, Float32Array>();\n  for (const [path, { sum, count }] of byPath) {\n    const avg = new Float32Array(sum.length);\n    for (let i = 0; i < sum.length; i++) {\n      avg[i] = sum[i] / count;\n    }\n    result.set(path, avg);\n  }\n  return result;\n}\n\nfunction getFileTags(db: Database, projectId: number, path: string): Set<string> {\n  const rows = db\n    .prepare(\n      `SELECT text FROM memory_chunks\n       WHERE project_id = ? 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AND target_path IS NOT NULL`,\n    )\n    .all(opts.notePath) as Array<{ target_path: string }>;\n  const linkedPaths = new Set(outboundRows.map((r) => r.target_path));\n\n  // Step 2: get source embedding\n  const sourceEmbedding = getFileAvgEmbedding(db, opts.vaultProjectId, opts.notePath);\n\n  // Step 3a: get all file-level embeddings for semantic scoring\n  const allEmbeddings = getAllFileEmbeddings(db, opts.vaultProjectId);\n  allEmbeddings.delete(opts.notePath);\n\n  // Step 3b: get source tags\n  const sourceTags = getFileTags(db, opts.vaultProjectId, opts.notePath);\n\n  // Step 3c: compute graph neighborhood (friends-of-friends)\n  const friendTargetRows = db\n    .prepare(\n      `SELECT DISTINCT target_path AS path FROM vault_links\n       WHERE source_path IN (\n         SELECT target_path FROM vault_links\n         WHERE source_path = ? AND target_path IS NOT NULL\n       ) AND target_path IS NOT NULL`,\n    )\n    .all(opts.notePath) as Array<{ path: string }>;\n\n  // For each friend-of-friend, count how many of source's direct friends link to them\n  const friendLinkCounts = new Map<string, number>();\n  for (const { path } of friendTargetRows) {\n    if (path === opts.notePath) continue;\n    friendLinkCounts.set(path, (friendLinkCounts.get(path) ?? 0) + 1);\n  }\n  const maxFriendLinks = Math.max(1, ...friendLinkCounts.values());\n\n  // Get all vault files to enumerate candidates\n  const allFiles = db\n    .prepare(\"SELECT vault_path, title FROM vault_files\")\n    .all() as Array<{ vault_path: string; title: string | null }>;\n\n  const suggestions: Suggestion[] = [];\n\n  for (const { vault_path, title } of allFiles) {\n    if (vault_path === opts.notePath) continue;\n    if (excludeLinked && linkedPaths.has(vault_path)) continue;\n\n    // Semantic score\n    let semanticScore = 0;\n    if (sourceEmbedding) 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 title,\n      score,\n      semanticScore,\n      tagScore,\n      neighborScore,\n      reason,\n      suggestedWikilink: suggestedWikilink(vault_path),\n    });\n  }\n\n  suggestions.sort((a, b) => b.score - a.score);\n  return suggestions.slice(0, 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+{"version":3,"file":"zettelkasten-e-a4rW_6.mjs","names":["MAX_CHUNKS","MAX_CHUNKS"],"sources":["../src/zettelkasten/explore.ts","../src/zettelkasten/surprise.ts","../src/zettelkasten/converse.ts","../src/zettelkasten/themes.ts","../src/zettelkasten/health.ts","../src/zettelkasten/suggest.ts"],"sourcesContent":["import type { Database } from \"better-sqlite3\";\nimport { dirname } from \"node:path\";\n\nexport interface ExploreOptions {\n  startNote: string;\n  depth?: number;\n  direction?: \"forward\" | \"backward\" | \"both\";\n  mode?: \"sequential\" | \"associative\" | \"all\";\n}\n\nexport interface ExploreNode {\n  path: string;\n  title: string | null;\n  depth: number;\n  linkType: \"sequential\" | \"associative\";\n  inbound: number;\n  outbound: number;\n}\n\nexport interface ExploreResult {\n  root: string;\n  nodes: ExploreNode[];\n  edges: Array<{ from: string; to: string; type: \"sequential\" | \"associative\" }>;\n  branchingPoints: string[];\n  maxDepthReached: boolean;\n}\n\nfunction classifyEdge(source: string, target: string): \"sequential\" | \"associative\" {\n  return dirname(source) === dirname(target) ? \"sequential\" : \"associative\";\n}\n\nfunction resolveStart(db: Database, startNote: string): string | null {\n  const inFiles = db\n    .prepare(\"SELECT vault_path FROM vault_files WHERE vault_path = ?\")\n    .get(startNote) as { vault_path: string } | undefined;\n  if (inFiles) return inFiles.vault_path;\n\n  const alias = db\n    .prepare(\"SELECT canonical_path FROM vault_aliases WHERE vault_path = ?\")\n    .get(startNote) as { canonical_path: string } | undefined;\n  if (!alias) return null;\n\n  const canonical = db\n    .prepare(\"SELECT vault_path FROM vault_files WHERE vault_path = ?\")\n    .get(alias.canonical_path) as { vault_path: string } | undefined;\n  return canonical ? canonical.vault_path : null;\n}\n\nfunction getForwardNeighbors(db: Database, path: string): string[] {\n  return (\n    db\n      .prepare(\n        \"SELECT target_path FROM vault_links WHERE source_path = ? AND target_path IS NOT NULL\",\n      )\n      .all(path) as Array<{ target_path: string }>\n  ).map((r) => r.target_path);\n}\n\nfunction getBackwardNeighbors(db: Database, path: string): string[] {\n  return (\n    db\n      .prepare(\n        \"SELECT source_path FROM vault_links WHERE target_path = ?\",\n      )\n      .all(path) as Array<{ source_path: string }>\n  ).map((r) => r.source_path);\n}\n\nfunction getFileInfo(\n  db: Database,\n  path: string,\n): { title: string | null; inbound: number; outbound: number } {\n  const file = db\n    .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n    .get(path) as { title: string | null } | undefined;\n\n  const health = db\n    .prepare(\"SELECT inbound_count, outbound_count FROM vault_health WHERE vault_path = ?\")\n    .get(path) as { inbound_count: number; outbound_count: number } | undefined;\n\n  return {\n    title: file?.title ?? null,\n    inbound: health?.inbound_count ?? 0,\n    outbound: health?.outbound_count ?? 0,\n  };\n}\n\n/**\n * Traverse the Zettelkasten link graph using BFS, following chains of thought\n * from a starting note up to a configurable depth.\n */\nexport function zettelExplore(db: Database, opts: ExploreOptions): ExploreResult {\n  const depth = Math.min(Math.max(opts.depth ?? 3, 1), 10);\n  const direction = opts.direction ?? \"both\";\n  const mode = opts.mode ?? \"all\";\n\n  const root = resolveStart(db, opts.startNote);\n  if (!root) {\n    return {\n      root: opts.startNote,\n      nodes: [],\n      edges: [],\n      branchingPoints: [],\n      maxDepthReached: false,\n    };\n  }\n\n  const visited = new Set<string>([root]);\n  const nodes: ExploreNode[] = [];\n  const edges: Array<{ from: string; to: string; type: \"sequential\" | \"associative\" }> = [];\n  let maxDepthReached = false;\n\n  const queue: Array<{ path: string; depth: number }> = [{ path: root, depth: 0 }];\n\n  while (queue.length > 0) {\n    const current = queue.shift()!;\n\n    if (current.depth >= depth) {\n      maxDepthReached = true;\n      continue;\n    }\n\n    const neighbors: Array<{ neighbor: string; from: string; to: string }> = [];\n\n    if (direction === \"forward\" || direction === \"both\") {\n      for (const n of getForwardNeighbors(db, current.path)) {\n        neighbors.push({ neighbor: n, from: current.path, to: n });\n      }\n    }\n\n    if (direction === \"backward\" || direction === \"both\") {\n      for (const n of getBackwardNeighbors(db, current.path)) {\n        neighbors.push({ neighbor: n, from: n, to: current.path });\n      }\n    }\n\n    for (const { neighbor, from, to } of neighbors) {\n      const edgeType = classifyEdge(from, to);\n\n      if (mode !== \"all\" && edgeType !== mode) {\n        continue;\n      }\n\n      const edgeKey = `${from}|${to}`;\n      const alreadyHasEdge = edges.some((e) => e.from === from && e.to === to);\n      if (!alreadyHasEdge) {\n        edges.push({ from, to, type: edgeType });\n      }\n\n      if (!visited.has(neighbor)) {\n        visited.add(neighbor);\n\n        const info = getFileInfo(db, neighbor);\n        nodes.push({\n          path: neighbor,\n          title: info.title,\n          depth: current.depth + 1,\n          linkType: edgeType,\n          inbound: info.inbound,\n          outbound: info.outbound,\n        });\n\n        queue.push({ path: neighbor, depth: current.depth + 1 });\n      }\n    }\n  }\n\n  const branchingPoints = nodes\n    .filter((n) => n.outbound > 2)\n    .map((n) => n.path);\n\n  const rootInfo = getFileInfo(db, root);\n  if (rootInfo.outbound > 2) {\n    branchingPoints.unshift(root);\n  }\n\n  return { root, nodes, edges, branchingPoints, maxDepthReached };\n}\n","import type { Database } from \"better-sqlite3\";\nimport {\n  deserializeEmbedding,\n  generateEmbedding,\n  cosineSimilarity,\n} from \"../memory/embeddings.js\";\n\nexport interface SurpriseOptions {\n  referencePath: string;\n  vaultProjectId: number;\n  limit?: number;\n  minSimilarity?: number;\n  minGraphDistance?: number;\n}\n\nexport interface SurpriseResult {\n  path: string;\n  title: string | null;\n  cosineSimilarity: number;\n  graphDistance: number;\n  surpriseScore: number;\n  sharedSnippet: string;\n}\n\nconst CHUNK_BATCH_SIZE = 500;\nconst MAX_CHUNKS = 5000;\nconst BFS_HOP_CAP = 20;\n\nfunction getFileEmbeddings(\n  db: Database,\n  projectId: number,\n): Map<string, { embedding: Float32Array; text: string }> {\n  const rows = db\n    .prepare(\n      `SELECT path, embedding, text FROM memory_chunks\n       WHERE project_id = ? AND embedding IS NOT NULL\n       ORDER BY path, start_line\n       LIMIT ?`,\n    )\n    .all(projectId, MAX_CHUNKS) as Array<{\n    path: string;\n    embedding: Buffer;\n    text: string;\n  }>;\n\n  // Group chunks by path and accumulate embeddings for averaging\n  const byPath = new Map<string, { sum: Float32Array; count: number; text: string }>();\n\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const entry = byPath.get(row.path);\n    if (!entry) {\n      byPath.set(row.path, { sum: new Float32Array(vec), count: 1, text: row.text });\n    } else {\n      for (let i = 0; i < vec.length; i++) {\n        entry.sum[i] += vec[i];\n      }\n      entry.count++;\n    }\n  }\n\n  const result = new Map<string, { embedding: Float32Array; text: string }>();\n  for (const [path, { sum, count, text }] of byPath) {\n    const avg = new Float32Array(sum.length);\n    for (let i = 0; i < sum.length; i++) {\n      avg[i] = sum[i] / count;\n    }\n    result.set(path, { embedding: avg, text });\n  }\n  return result;\n}\n\nfunction getReferenceEmbedding(\n  db: Database,\n  projectId: number,\n  path: string,\n): { embedding: Float32Array; found: boolean } {\n  const rows = db\n    .prepare(\n      `SELECT embedding FROM memory_chunks\n       WHERE project_id = ? AND path = ? AND embedding IS NOT NULL`,\n    )\n    .all(projectId, path) as Array<{ embedding: Buffer }>;\n\n  if (rows.length === 0) {\n    return { embedding: new Float32Array(0), found: false };\n  }\n\n  const dim = deserializeEmbedding(rows[0].embedding).length;\n  const sum = new Float32Array(dim);\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    for (let i = 0; i < dim; i++) {\n      sum[i] += vec[i];\n    }\n  }\n  const avg = new Float32Array(dim);\n  for (let i = 0; i < dim; i++) {\n    avg[i] = sum[i] / rows.length;\n  }\n  return { embedding: avg, found: true };\n}\n\nfunction bfsGraphDistance(db: Database, source: string, target: string): number {\n  if (source === target) return 0;\n\n  const visited = new Set<string>([source]);\n  const queue: Array<{ path: string; hops: number }> = [{ path: source, hops: 0 }];\n\n  while (queue.length > 0) {\n    const { path, hops } = queue.shift()!;\n    if (hops >= BFS_HOP_CAP) continue;\n\n    const neighbors = db\n      .prepare(\n        `SELECT target_path AS neighbor FROM vault_links\n         WHERE source_path = ? AND target_path IS NOT NULL\n         UNION\n         SELECT source_path AS neighbor FROM vault_links\n         WHERE target_path = ?`,\n      )\n      .all(path, path) as Array<{ neighbor: string }>;\n\n    for (const { neighbor } of neighbors) {\n      if (neighbor === target) return hops + 1;\n      if (!visited.has(neighbor)) {\n        visited.add(neighbor);\n        queue.push({ path: neighbor, hops: hops + 1 });\n      }\n    }\n  }\n\n  return Infinity;\n}\n\nfunction getBestChunkText(\n  db: Database,\n  projectId: number,\n  path: string,\n  refEmbedding: Float32Array,\n): string {\n  const rows = db\n    .prepare(\n      `SELECT text, embedding FROM memory_chunks\n       WHERE project_id = ? AND path = ? AND embedding IS NOT NULL\n       LIMIT 20`,\n    )\n    .all(projectId, path) as Array<{ text: string; embedding: Buffer }>;\n\n  if (rows.length === 0) return \"\";\n\n  let bestText = rows[0].text;\n  let bestSim = -Infinity;\n\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const sim = cosineSimilarity(refEmbedding, vec);\n    if (sim > bestSim) {\n      bestSim = sim;\n      bestText = row.text;\n    }\n  }\n\n  return bestText.trim().slice(0, 200);\n}\n\n/**\n * Find notes that are semantically similar to a reference note but graph-distant —\n * revealing surprising conceptual connections across unrelated areas of the Zettelkasten.\n */\nexport async function zettelSurprise(\n  db: Database,\n  opts: SurpriseOptions,\n): Promise<SurpriseResult[]> {\n  const limit = opts.limit ?? 10;\n  const minSimilarity = opts.minSimilarity ?? 0.3;\n  const minGraphDistance = opts.minGraphDistance ?? 3;\n\n  let { embedding: refEmbedding, found } = getReferenceEmbedding(\n    db,\n    opts.vaultProjectId,\n    opts.referencePath,\n  );\n\n  // Fall back to generating an embedding from the file title if no chunks exist\n  if (!found) {\n    const file = db\n      .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n      .get(opts.referencePath) as { title: string | null } | undefined;\n    const text = file?.title ?? opts.referencePath;\n    refEmbedding = await generateEmbedding(text, true);\n  }\n\n  const allFileEmbeddings = getFileEmbeddings(db, opts.vaultProjectId);\n\n  // Remove the reference note itself from candidates\n  allFileEmbeddings.delete(opts.referencePath);\n\n  // First pass: filter by semantic similarity to avoid BFS on all nodes\n  const semanticCandidates: Array<{ path: string; sim: number }> = [];\n  for (const [path, { embedding }] of allFileEmbeddings) {\n    const sim = cosineSimilarity(refEmbedding, embedding);\n    if (sim >= minSimilarity) {\n      semanticCandidates.push({ path, sim });\n    }\n  }\n\n  // Compute graph distances for semantic candidates\n  const results: SurpriseResult[] = [];\n\n  for (const { path, sim } of semanticCandidates) {\n    const graphDistance = bfsGraphDistance(db, opts.referencePath, path);\n\n    const effectiveDistance = isFinite(graphDistance) ? graphDistance : BFS_HOP_CAP;\n    if (effectiveDistance < minGraphDistance) continue;\n\n    const file = db\n      .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n      .get(path) as { title: string | null } | undefined;\n\n    const surpriseScore = sim * Math.log2(effectiveDistance + 1);\n    const sharedSnippet = getBestChunkText(db, opts.vaultProjectId, path, refEmbedding);\n\n    results.push({\n      path,\n      title: file?.title ?? null,\n      cosineSimilarity: sim,\n      graphDistance: isFinite(graphDistance) ? graphDistance : Infinity,\n      surpriseScore,\n      sharedSnippet,\n    });\n  }\n\n  results.sort((a, b) => b.surpriseScore - a.surpriseScore);\n  return results.slice(0, limit);\n}\n","import type { Database } from \"better-sqlite3\";\nimport { searchMemoryHybrid } from \"../memory/search.js\";\nimport { generateEmbedding } from \"../memory/embeddings.js\";\n\nexport interface ConverseOptions {\n  /** The user's question or topic to explore. */\n  question: string;\n  /** project_id for vault chunks in memory_chunks. */\n  vaultProjectId: number;\n  /** Graph expansion depth. Default 2. */\n  depth?: number;\n  /** Maximum number of relevant notes to return. Default 15. */\n  limit?: number;\n}\n\nexport interface ConverseConnection {\n  fromPath: string;\n  toPath: string;\n  /** Top-level folder of fromPath. */\n  fromDomain: string;\n  /** Top-level folder of toPath. */\n  toDomain: string;\n  /** Link count between these two notes (can be > 1). */\n  strength: number;\n}\n\nexport interface ConverseResult {\n  relevantNotes: Array<{\n    path: string;\n    title: string | null;\n    snippet: string;\n    score: number;\n    domain: string;\n  }>;\n  /** Cross-domain connections found among the selected notes. */\n  connections: ConverseConnection[];\n  /** Unique domains involved across all selected notes. */\n  domains: string[];\n  /** AI-ready prompt combining notes + connections for insight generation. */\n  synthesisPrompt: string;\n}\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Extract the top-level folder from a vault path (first path segment). */\nfunction extractDomain(vaultPath: string): string {\n  const slash = vaultPath.indexOf(\"/\");\n  return slash === -1 ? vaultPath : vaultPath.slice(0, slash);\n}\n\n/**\n * Expand one level of graph neighbors for a set of paths.\n * Returns all outbound and inbound neighbor paths (excluding already-visited).\n */\nfunction expandNeighbors(db: Database, paths: Set<string>): string[] {\n  if (paths.size === 0) return [];\n\n  const placeholders = Array.from(paths).map(() => \"?\").join(\", \");\n  const pathList = Array.from(paths);\n\n  const forward = db\n    .prepare(\n      `SELECT DISTINCT target_path FROM vault_links WHERE source_path IN (${placeholders}) AND target_path IS NOT NULL`,\n    )\n    .all(...pathList) as Array<{ target_path: string }>;\n\n  const backward = db\n    .prepare(\n      `SELECT DISTINCT source_path FROM vault_links WHERE target_path IN (${placeholders})`,\n    )\n    .all(...pathList) as Array<{ source_path: string }>;\n\n  const neighbors: string[] = [];\n  for (const r of forward) neighbors.push(r.target_path);\n  for (const r of backward) neighbors.push(r.source_path);\n  return neighbors;\n}\n\n/**\n * Look up the title for a single vault path.\n * Returns null when the path is not found in vault_files.\n */\nfunction getTitle(db: Database, path: string): string | null {\n  const row = db\n    .prepare(\"SELECT title FROM vault_files WHERE vault_path = ?\")\n    .get(path) as { title: string | null } | undefined;\n  return row?.title ?? null;\n}\n\n/**\n * Count inbound links for a path from vault_health.\n * Used as a tiebreaker when trimming neighbor-only notes.\n */\nfunction getInboundCount(db: Database, path: string): number {\n  const row = db\n    .prepare(\"SELECT inbound_count FROM vault_health WHERE vault_path = ?\")\n    .get(path) as { inbound_count: number } | undefined;\n  return row?.inbound_count ?? 0;\n}\n\n// ---------------------------------------------------------------------------\n// Main export\n// ---------------------------------------------------------------------------\n\n/**\n * Let the vault \"talk back\" — find notes relevant to a question, expand\n * through the link graph, identify cross-domain connections, and return a\n * structured result including a synthesis prompt for an AI to generate insights.\n */\nexport async function zettelConverse(\n  db: Database,\n  opts: ConverseOptions,\n): Promise<ConverseResult> {\n  const depth = Math.max(opts.depth ?? 2, 0);\n  const limit = Math.max(opts.limit ?? 15, 1);\n  const candidateLimit = 20;\n\n  // ------------------------------------------------------------------\n  // 1. Hybrid search: find top candidates via BM25 + semantic similarity\n  // ------------------------------------------------------------------\n  const queryEmbedding = await generateEmbedding(opts.question, true);\n\n  const searchResults = searchMemoryHybrid(\n    db,\n    opts.question,\n    queryEmbedding,\n    {\n      projectIds: [opts.vaultProjectId],\n      maxResults: candidateLimit,\n    },\n  );\n\n  // Map of path -> best score + snippet from search results\n  const searchHits = new Map<string, { score: number; snippet: string }>();\n  for (const r of searchResults) {\n    const existing = searchHits.get(r.path);\n    if (!existing || r.score > existing.score) {\n      searchHits.set(r.path, { score: r.score, snippet: r.snippet });\n    }\n  }\n\n  // ------------------------------------------------------------------\n  // 2. Graph expansion: BFS from each search result up to `depth` levels\n  // ------------------------------------------------------------------\n  const allPaths = new Set<string>(searchHits.keys());\n  let frontier = new Set<string>(searchHits.keys());\n\n  for (let d = 0; d < depth; d++) {\n    const neighbors = expandNeighbors(db, frontier);\n    const newFrontier = new Set<string>();\n    for (const n of neighbors) {\n      if (!allPaths.has(n)) {\n        allPaths.add(n);\n        newFrontier.add(n);\n      }\n    }\n    if (newFrontier.size === 0) break;\n    frontier = newFrontier;\n  }\n\n  // ------------------------------------------------------------------\n  // 3. Deduplicate + trim to limit\n  //    Search results first (ranked by score), then neighbors by inbound count\n  // ------------------------------------------------------------------\n  const searchRanked = Array.from(searchHits.entries())\n    .sort((a, b) => b[1].score - a[1].score)\n    .map(([path, info]) => ({ path, ...info, isSearchResult: true }));\n\n  const neighborPaths = Array.from(allPaths).filter((p) => !searchHits.has(p));\n\n  // Sort neighbors by link popularity (inbound count) so that well-connected\n  // notes are preferred when we have budget for them.\n  const neighborRanked = neighborPaths\n    .map((path) => ({\n      path,\n      score: 0,\n      snippet: \"\",\n      inbound: getInboundCount(db, path),\n      isSearchResult: false,\n    }))\n    .sort((a, b) => b.inbound - a.inbound);\n\n  // Combine: search results fill the budget first, then neighbors\n  const budgetForNeighbors = Math.max(limit - searchRanked.length, 0);\n  const selectedNeighbors = neighborRanked.slice(0, budgetForNeighbors);\n\n  const selectedSearchPaths = searchRanked.slice(0, limit);\n  const selectedPaths = new Set<string>([\n    ...selectedSearchPaths.map((r) => r.path),\n    ...selectedNeighbors.map((r) => r.path),\n  ]);\n\n  // ------------------------------------------------------------------\n  // 4. Build relevantNotes with titles + domains\n  // ------------------------------------------------------------------\n  const relevantNotes: ConverseResult[\"relevantNotes\"] = [];\n\n  for (const r of selectedSearchPaths) {\n    if (!selectedPaths.has(r.path)) continue;\n    relevantNotes.push({\n      path: r.path,\n      title: getTitle(db, r.path),\n      snippet: r.snippet,\n      score: r.score,\n      domain: extractDomain(r.path),\n    });\n  }\n\n  for (const r of selectedNeighbors) {\n    relevantNotes.push({\n      path: r.path,\n      title: getTitle(db, r.path),\n      snippet: r.snippet,\n      score: 0,\n      domain: extractDomain(r.path),\n    });\n  }\n\n  // ------------------------------------------------------------------\n  // 5. Find connections between the selected notes\n  // ------------------------------------------------------------------\n  let connections: ConverseConnection[] = [];\n\n  if (selectedPaths.size > 0) {\n    const pathList = Array.from(selectedPaths);\n    const placeholders = pathList.map(() => \"?\").join(\", \");\n\n    const edgeRows = db\n      .prepare(\n        `SELECT source_path, target_path, COUNT(*) AS cnt\n         FROM vault_links\n         WHERE source_path IN (${placeholders})\n           AND target_path IN (${placeholders})\n         GROUP BY source_path, target_path`,\n      )\n      .all(...pathList, ...pathList) as Array<{\n        source_path: string;\n        target_path: string;\n        cnt: number;\n      }>;\n\n    for (const row of edgeRows) {\n      connections.push({\n        fromPath: row.source_path,\n        toPath: row.target_path,\n        fromDomain: extractDomain(row.source_path),\n        toDomain: extractDomain(row.target_path),\n        strength: row.cnt,\n      });\n    }\n  }\n\n  // ------------------------------------------------------------------\n  // 6. Domains + cross-domain filter\n  // ------------------------------------------------------------------\n  const domainSet = new Set<string>(relevantNotes.map((n) => n.domain));\n  const domains = Array.from(domainSet).sort();\n\n  const crossDomainConnections = connections.filter(\n    (c) => c.fromDomain !== c.toDomain,\n  );\n\n  // ------------------------------------------------------------------\n  // 7. Build synthesis prompt\n  // ------------------------------------------------------------------\n  const notesSummary = relevantNotes\n    .map((n, i) => {\n      const title = n.title ? `\"${n.title}\"` : \"(untitled)\";\n      const domain = n.domain;\n      const scoreLabel = n.score > 0 ? ` [relevance: ${n.score.toFixed(3)}]` : \" [context]\";\n      const snippet = n.snippet.trim().slice(0, 300);\n      return `${i + 1}. [${domain}] ${title}${scoreLabel}\\n   Path: ${n.path}\\n   \"${snippet}\"`;\n    })\n    .join(\"\\n\\n\");\n\n  const connectionSummary =\n    crossDomainConnections.length > 0\n      ? crossDomainConnections\n          .map(\n            (c) =>\n              `- \"${c.fromPath}\" (${c.fromDomain}) → \"${c.toPath}\" (${c.toDomain}) [strength: ${c.strength}]`,\n          )\n          .join(\"\\n\")\n      : \"(no cross-domain connections found)\";\n\n  const domainList = domains.join(\", \");\n\n  const synthesisPrompt = `You are a Zettelkasten research assistant. The vault has surfaced the following notes in response to this question:\n\nQUESTION: ${opts.question}\n\n---\n\nRELEVANT NOTES (${relevantNotes.length} notes across ${domains.length} domain(s): ${domainList}):\n\n${notesSummary}\n\n---\n\nCROSS-DOMAIN CONNECTIONS (links bridging different knowledge areas):\n\n${connectionSummary}\n\n---\n\nSYNTHESIS TASK:\n\nBased on these notes and the connections between them, please:\n\n1. Identify the key insights that emerge in direct response to the question.\n2. Highlight any unexpected connections between notes from different domains (${domainList}).\n3. Point out tensions, contradictions, or open questions the vault raises but does not resolve.\n4. Suggest what is notably absent — what the vault does NOT yet contain that would strengthen the understanding of this topic.\n5. Propose 2-3 new notes that would meaningfully extend this knowledge cluster.\n\nThink like a scholar who has deeply internalized these ideas and is now synthesizing them for the first time.`;\n\n  return {\n    relevantNotes,\n    connections: crossDomainConnections,\n    domains,\n    synthesisPrompt,\n  };\n}\n","import type { Database } from \"better-sqlite3\";\nimport { deserializeEmbedding, cosineSimilarity } from \"../memory/embeddings.js\";\n\nexport interface ThemeOptions {\n  vaultProjectId: number;\n  lookbackDays?: number;\n  minClusterSize?: number;\n  maxThemes?: number;\n  similarityThreshold?: number;\n}\n\nexport interface ThemeCluster {\n  id: number;\n  label: string;\n  notes: Array<{\n    path: string;\n    title: string | null;\n  }>;\n  size: number;\n  folderDiversity: number;\n  avgRecency: number;\n  linkedRatio: number;\n  suggestIndexNote: boolean;\n}\n\nexport interface ThemeResult {\n  themes: ThemeCluster[];\n  totalNotesAnalyzed: number;\n  timeWindow: { from: number; to: number };\n}\n\nconst MAX_CHUNKS = 5000;\n\nconst STOP_WORDS = new Set([\n  \"a\", \"an\", \"the\", \"and\", \"or\", \"but\", \"in\", \"on\", \"at\", \"to\", \"for\",\n  \"of\", \"with\", \"by\", \"from\", \"is\", \"it\", \"as\", \"be\", \"was\", \"are\",\n  \"has\", \"had\", \"have\", \"not\", \"this\", \"that\", \"i\", \"my\", \"we\", \"our\",\n  \"new\", \"note\", \"untitled\", \"page\", \"file\", \"doc\",\n]);\n\nfunction getTopFolder(vaultPath: string): string {\n  const parts = vaultPath.split(\"/\");\n  return parts.length > 1 ? parts[0] : \"\";\n}\n\nfunction generateLabel(titles: Array<string | null>): string {\n  const wordCounts = new Map<string, number>();\n  for (const title of titles) {\n    if (!title) continue;\n    const words = title\n      .toLowerCase()\n      .replace(/[^a-z0-9\\s]/g, \" \")\n      .split(/\\s+/)\n      .filter((w) => w.length > 2 && !STOP_WORDS.has(w));\n    for (const word of words) {\n      wordCounts.set(word, (wordCounts.get(word) ?? 0) + 1);\n    }\n  }\n  const sorted = [...wordCounts.entries()].sort((a, b) => b[1] - a[1]);\n  return sorted\n    .slice(0, 3)\n    .map(([w]) => w)\n    .join(\" / \");\n}\n\nfunction computeLinkedRatio(db: Database, paths: string[]): number {\n  if (paths.length < 2) return 0;\n  const totalPairs = (paths.length * (paths.length - 1)) / 2;\n  const pathSet = new Set(paths);\n  let linkedPairs = 0;\n\n  for (const path of paths) {\n    const rows = db\n      .prepare(\n        `SELECT target_path FROM vault_links\n         WHERE source_path = ? AND target_path IS NOT NULL`,\n      )\n      .all(path) as Array<{ target_path: string }>;\n    for (const { target_path } of rows) {\n      if (pathSet.has(target_path)) {\n        linkedPairs++;\n      }\n    }\n  }\n\n  // Each bidirectional pair might be counted once per direction; divide by 2 to normalize\n  const uniquePairs = linkedPairs / 2;\n  return Math.min(1, uniquePairs / totalPairs);\n}\n\ntype ClusterNode = {\n  paths: string[];\n  titles: Array<string | null>;\n  indexedAts: number[];\n  centroid: Float32Array;\n};\n\nfunction averageEmbeddings(embeddings: Float32Array[]): Float32Array {\n  if (embeddings.length === 0) return new Float32Array(0);\n  const dim = embeddings[0].length;\n  const sum = new Float32Array(dim);\n  for (const vec of embeddings) {\n    for (let i = 0; i < dim; i++) {\n      sum[i] += vec[i];\n    }\n  }\n  const avg = new Float32Array(dim);\n  for (let i = 0; i < dim; i++) {\n    avg[i] = sum[i] / embeddings.length;\n  }\n  return avg;\n}\n\n/**\n * Detect emerging themes in recently-modified notes using agglomerative single-linkage\n * clustering of note-level embeddings.\n */\nexport async function zettelThemes(\n  db: Database,\n  opts: ThemeOptions,\n): Promise<ThemeResult> {\n  const lookbackDays = opts.lookbackDays ?? 30;\n  const minClusterSize = opts.minClusterSize ?? 3;\n  const maxThemes = opts.maxThemes ?? 10;\n  const similarityThreshold = opts.similarityThreshold ?? 0.65;\n\n  const now = Date.now();\n  const from = now - lookbackDays * 86400000;\n\n  // Step 1: get recent notes\n  const recentNotes = db\n    .prepare(\n      `SELECT vault_path, title, indexed_at FROM vault_files WHERE indexed_at > ?`,\n    )\n    .all(from) as Array<{ vault_path: string; title: string | null; indexed_at: number }>;\n\n  // Step 2: get file-level embeddings from memory_chunks\n  const chunkRows = db\n    .prepare(\n      `SELECT path, embedding FROM memory_chunks\n       WHERE project_id = ? AND embedding IS NOT NULL\n       ORDER BY path, start_line\n       LIMIT ?`,\n    )\n    .all(opts.vaultProjectId, MAX_CHUNKS) as Array<{ path: string; embedding: Buffer }>;\n\n  const embeddingsByPath = new Map<string, Float32Array[]>();\n  for (const row of chunkRows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const arr = embeddingsByPath.get(row.path);\n    if (!arr) {\n      embeddingsByPath.set(row.path, [vec]);\n    } else {\n      arr.push(vec);\n    }\n  }\n\n  const fileEmbeddings = new Map<string, Float32Array>();\n  for (const [path, vecs] of embeddingsByPath) {\n    fileEmbeddings.set(path, averageEmbeddings(vecs));\n  }\n\n  // Step 3: build initial clusters — only include notes that have embeddings\n  const clusters: ClusterNode[] = [];\n  for (const note of recentNotes) {\n    const embedding = fileEmbeddings.get(note.vault_path);\n    if (!embedding) continue;\n    clusters.push({\n      paths: [note.vault_path],\n      titles: [note.title],\n      indexedAts: [note.indexed_at],\n      centroid: embedding,\n    });\n  }\n\n  const totalNotesAnalyzed = clusters.length;\n\n  // Step 4: agglomerative single-linkage clustering\n  // Stop when no two clusters have similarity >= threshold\n  // Using centroid similarity as a proxy for single-linkage max similarity\n  let merged = true;\n  while (merged && clusters.length > 1) {\n    merged = false;\n    let bestSim = similarityThreshold;\n    let bestI = -1;\n    let bestJ = -1;\n\n    for (let i = 0; i < clusters.length; i++) {\n      for (let j = i + 1; j < clusters.length; j++) {\n        const sim = cosineSimilarity(clusters[i].centroid, clusters[j].centroid);\n        if (sim > bestSim) {\n          bestSim = sim;\n          bestI = i;\n          bestJ = j;\n        }\n      }\n    }\n\n    if (bestI === -1) break;\n\n    // Merge cluster j into cluster i\n    const ci = clusters[bestI];\n    const cj = clusters[bestJ];\n    const mergedPaths = [...ci.paths, ...cj.paths];\n    const mergedTitles = [...ci.titles, ...cj.titles];\n    const mergedIndexedAts = [...ci.indexedAts, ...cj.indexedAts];\n\n    // Recompute centroid from averaged embeddings of all member paths\n    const memberEmbeddings: Float32Array[] = [];\n    for (const p of mergedPaths) {\n      const emb = fileEmbeddings.get(p);\n      if (emb) memberEmbeddings.push(emb);\n    }\n\n    clusters[bestI] = {\n      paths: mergedPaths,\n      titles: mergedTitles,\n      indexedAts: mergedIndexedAts,\n      centroid: averageEmbeddings(memberEmbeddings),\n    };\n\n    clusters.splice(bestJ, 1);\n    merged = true;\n  }\n\n  // Step 5: filter and annotate clusters\n  const themes: ThemeCluster[] = [];\n  let clusterIndex = 0;\n\n  for (const cluster of clusters) {\n    if (cluster.paths.length < minClusterSize) continue;\n\n    const label = generateLabel(cluster.titles) || `Theme ${clusterIndex + 1}`;\n    const avgRecency =\n      cluster.indexedAts.reduce((sum, t) => sum + t, 0) / cluster.indexedAts.length;\n\n    const uniqueFolders = new Set(cluster.paths.map(getTopFolder));\n    const folderDiversity = uniqueFolders.size / cluster.paths.length;\n\n    const linkedRatio = computeLinkedRatio(db, cluster.paths);\n    const suggestIndexNote = linkedRatio < 0.3 && cluster.paths.length >= 5;\n\n    themes.push({\n      id: clusterIndex++,\n      label,\n      notes: cluster.paths.map((path, idx) => ({\n        path,\n        title: cluster.titles[idx],\n      })),\n      size: cluster.paths.length,\n      folderDiversity,\n      avgRecency,\n      linkedRatio,\n      suggestIndexNote,\n    });\n  }\n\n  // Step 6: rank by size * folderDiversity * recency_ratio\n  themes.sort(\n    (a, b) =>\n      b.size * b.folderDiversity * (b.avgRecency / now) -\n      a.size * a.folderDiversity * (a.avgRecency / now),\n  );\n\n  return {\n    themes: themes.slice(0, maxThemes),\n    totalNotesAnalyzed,\n    timeWindow: { from, to: now },\n  };\n}\n","import type { Database } from \"better-sqlite3\";\n\nexport interface HealthOptions {\n  scope?: \"full\" | \"recent\" | \"project\";\n  projectPath?: string;\n  recentDays?: number;\n  include?: Array<\"dead_links\" | \"orphans\" | \"disconnected\" | \"low_connectivity\">;\n}\n\nexport interface DeadLink {\n  sourcePath: string;\n  targetRaw: string;\n  lineNumber: number;\n}\n\nexport interface HealthResult {\n  totalFiles: number;\n  totalLinks: number;\n  deadLinks: DeadLink[];\n  orphans: string[];\n  disconnectedClusters: number;\n  lowConnectivity: string[];\n  healthScore: number;\n  computedAt: number;\n}\n\nfunction buildScopeFilter(\n  opts: HealthOptions,\n  tableAlias: string,\n  pathColumn: string,\n): { clause: string; params: unknown[] } {\n  const scope = opts.scope ?? \"full\";\n\n  if (scope === \"project\") {\n    const prefix = opts.projectPath ?? \"\";\n    return {\n      clause: `WHERE ${tableAlias}.${pathColumn} LIKE ? || '%'`,\n      params: [prefix],\n    };\n  }\n\n  if (scope === \"recent\") {\n    const days = opts.recentDays ?? 30;\n    const cutoff = Date.now() - days * 86400000;\n    return {\n      clause: `WHERE ${tableAlias}.indexed_at > ?`,\n      params: [cutoff],\n    };\n  }\n\n  return { clause: \"\", params: [] };\n}\n\nfunction countComponents(nodes: string[], edges: Array<{ source: string; target: string }>): number {\n  if (nodes.length === 0) return 0;\n\n  const parent = new Map<string, string>();\n  const rank = new Map<string, number>();\n\n  for (const n of nodes) {\n    parent.set(n, n);\n    rank.set(n, 0);\n  }\n\n  function find(x: string): string {\n    let root = x;\n    while (parent.get(root) !== root) {\n      root = parent.get(root)!;\n    }\n    let current = x;\n    while (current !== root) {\n      const next = parent.get(current)!;\n      parent.set(current, root);\n      current = next;\n    }\n    return root;\n  }\n\n  function union(a: string, b: string): void {\n    const ra = find(a);\n    const rb = find(b);\n    if (ra === rb) return;\n    const rankA = rank.get(ra) ?? 0;\n    const rankB = rank.get(rb) ?? 0;\n    if (rankA < rankB) {\n      parent.set(ra, rb);\n    } else if (rankA > rankB) {\n      parent.set(rb, ra);\n    } else {\n      parent.set(rb, ra);\n      rank.set(ra, rankA + 1);\n    }\n  }\n\n  for (const { source, target } of edges) {\n    if (parent.has(source) && parent.has(target)) {\n      union(source, target);\n    }\n  }\n\n  const roots = new Set<string>();\n  for (const n of nodes) {\n    roots.add(find(n));\n  }\n  return roots.size;\n}\n\n/**\n * Audit the structural health of the Zettelkasten vault using graph metrics.\n * Designed to complete in under 60ms for a full vault.\n */\nexport function zettelHealth(db: Database, opts?: HealthOptions): HealthResult {\n  const options = opts ?? {};\n  const scope = options.scope ?? \"full\";\n  const include = options.include ?? [\"dead_links\", \"orphans\", \"disconnected\", \"low_connectivity\"];\n\n  const computedAt = Date.now();\n\n  // --- totalFiles ---\n  let totalFiles = 0;\n  if (scope === \"full\") {\n    totalFiles = (\n      db.prepare(\"SELECT COUNT(*) AS n FROM vault_files\").get() as { n: number }\n    ).n;\n  } else if (scope === \"project\") {\n    const prefix = options.projectPath ?? \"\";\n    totalFiles = (\n      db\n        .prepare(\"SELECT COUNT(*) AS n FROM vault_files WHERE vault_path LIKE ? || '%'\")\n        .get(prefix) as { n: number }\n    ).n;\n  } else {\n    const days = options.recentDays ?? 30;\n    const cutoff = computedAt - days * 86400000;\n    totalFiles = (\n      db\n        .prepare(\"SELECT COUNT(*) AS n FROM vault_files WHERE indexed_at > ?\")\n        .get(cutoff) as { n: number }\n    ).n;\n  }\n\n  // --- totalLinks ---\n  let totalLinks = 0;\n  if (scope === \"full\") {\n    totalLinks = (\n      db.prepare(\"SELECT COUNT(*) AS n FROM vault_links\").get() as { n: number }\n    ).n;\n  } else if (scope === \"project\") {\n    const prefix = options.projectPath ?? \"\";\n    totalLinks = (\n      db\n        .prepare(\"SELECT COUNT(*) AS n FROM vault_links WHERE source_path LIKE ? || '%'\")\n        .get(prefix) as { n: number }\n    ).n;\n  } else {\n    const days = options.recentDays ?? 30;\n    const cutoff = computedAt - days * 86400000;\n    totalLinks = (\n      db\n        .prepare(\n          \"SELECT COUNT(*) AS n FROM vault_links WHERE source_path IN (SELECT vault_path FROM vault_files WHERE indexed_at > ?)\",\n        )\n        .get(cutoff) as { n: number }\n    ).n;\n  }\n\n  // --- deadLinks ---\n  let deadLinks: DeadLink[] = [];\n  if (include.includes(\"dead_links\")) {\n    if (scope === \"full\") {\n      deadLinks = (\n        db\n          .prepare(\n            \"SELECT source_path, target_raw, line_number FROM vault_links WHERE target_path IS NULL\",\n          )\n          .all() as Array<{ source_path: string; target_raw: string; line_number: number }>\n      ).map((r) => ({\n        sourcePath: r.source_path,\n        targetRaw: r.target_raw,\n        lineNumber: r.line_number,\n      }));\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      deadLinks = (\n        db\n          .prepare(\n            \"SELECT source_path, target_raw, line_number FROM vault_links WHERE target_path IS NULL AND source_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ source_path: string; target_raw: string; line_number: number }>\n      ).map((r) => ({\n        sourcePath: r.source_path,\n        targetRaw: r.target_raw,\n        lineNumber: r.line_number,\n      }));\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      deadLinks = (\n        db\n          .prepare(\n            \"SELECT source_path, target_raw, line_number FROM vault_links WHERE target_path IS NULL AND source_path IN (SELECT vault_path FROM vault_files WHERE indexed_at > ?)\",\n          )\n          .all(cutoff) as Array<{ source_path: string; target_raw: string; line_number: number }>\n      ).map((r) => ({\n        sourcePath: r.source_path,\n        targetRaw: r.target_raw,\n        lineNumber: r.line_number,\n      }));\n    }\n  }\n\n  // --- orphans ---\n  let orphans: string[] = [];\n  if (include.includes(\"orphans\")) {\n    if (scope === \"full\") {\n      orphans = (\n        db\n          .prepare(\"SELECT vault_path FROM vault_health WHERE is_orphan = 1\")\n          .all() as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      orphans = (\n        db\n          .prepare(\n            \"SELECT vault_path FROM vault_health WHERE is_orphan = 1 AND vault_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      orphans = (\n        db\n          .prepare(\n            \"SELECT vh.vault_path FROM vault_health vh JOIN vault_files vf ON vh.vault_path = vf.vault_path WHERE vh.is_orphan = 1 AND vf.indexed_at > ?\",\n          )\n          .all(cutoff) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    }\n  }\n\n  // --- disconnectedClusters (union-find) ---\n  let disconnectedClusters = 1;\n  if (include.includes(\"disconnected\")) {\n    let allNodes: string[];\n    let allEdges: Array<{ source: string; target: string }>;\n\n    if (scope === \"full\") {\n      allNodes = (\n        db.prepare(\"SELECT vault_path FROM vault_files\").all() as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n\n      allEdges = (\n        db\n          .prepare(\n            \"SELECT DISTINCT source_path AS source, target_path AS target FROM vault_links WHERE target_path IS NOT NULL\",\n          )\n          .all() as Array<{ source: string; target: string }>\n      );\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      allNodes = (\n        db\n          .prepare(\"SELECT vault_path FROM vault_files WHERE vault_path LIKE ? || '%'\")\n          .all(prefix) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n\n      allEdges = (\n        db\n          .prepare(\n            \"SELECT DISTINCT source_path AS source, target_path AS target FROM vault_links WHERE target_path IS NOT NULL AND source_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ source: string; target: string }>\n      );\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      allNodes = (\n        db\n          .prepare(\"SELECT vault_path FROM vault_files WHERE indexed_at > ?\")\n          .all(cutoff) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n\n      allEdges = (\n        db\n          .prepare(\n            \"SELECT DISTINCT source_path AS source, target_path AS target FROM vault_links WHERE target_path IS NOT NULL AND source_path IN (SELECT vault_path FROM vault_files WHERE indexed_at > ?)\",\n          )\n          .all(cutoff) as Array<{ source: string; target: string }>\n      );\n    }\n\n    disconnectedClusters = countComponents(allNodes, allEdges);\n  }\n\n  // --- lowConnectivity ---\n  let lowConnectivity: string[] = [];\n  if (include.includes(\"low_connectivity\")) {\n    if (scope === \"full\") {\n      lowConnectivity = (\n        db\n          .prepare(\n            \"SELECT vault_path FROM vault_health WHERE inbound_count + outbound_count <= 1\",\n          )\n          .all() as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else if (scope === \"project\") {\n      const prefix = options.projectPath ?? \"\";\n      lowConnectivity = (\n        db\n          .prepare(\n            \"SELECT vault_path FROM vault_health WHERE inbound_count + outbound_count <= 1 AND vault_path LIKE ? || '%'\",\n          )\n          .all(prefix) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    } else {\n      const days = options.recentDays ?? 30;\n      const cutoff = computedAt - days * 86400000;\n      lowConnectivity = (\n        db\n          .prepare(\n            \"SELECT vh.vault_path FROM vault_health vh JOIN vault_files vf ON vh.vault_path = vf.vault_path WHERE vh.inbound_count + vh.outbound_count <= 1 AND vf.indexed_at > ?\",\n          )\n          .all(cutoff) as Array<{ vault_path: string }>\n      ).map((r) => r.vault_path);\n    }\n  }\n\n  // --- healthScore ---\n  const deadRatio = totalLinks > 0 ? deadLinks.length / totalLinks : 0;\n  const orphanRatio = totalFiles > 0 ? orphans.length / totalFiles : 0;\n  const lowConnRatio = totalFiles > 0 ? lowConnectivity.length / totalFiles : 0;\n  const healthScore = Math.round(\n    100 * (1 - deadRatio) * (1 - orphanRatio * 0.5) * (1 - lowConnRatio * 0.3),\n  );\n\n  return {\n    totalFiles,\n    totalLinks,\n    deadLinks,\n    orphans,\n    disconnectedClusters,\n    lowConnectivity,\n    healthScore,\n    computedAt,\n  };\n}\n","import type { Database } from \"better-sqlite3\";\nimport { deserializeEmbedding, cosineSimilarity } from \"../memory/embeddings.js\";\nimport { basename } from \"node:path\";\n\nexport interface SuggestOptions {\n  notePath: string;\n  vaultProjectId: number;\n  limit?: number;\n  excludeLinked?: boolean;\n}\n\nexport interface Suggestion {\n  path: string;\n  title: string | null;\n  score: number;\n  semanticScore: number;\n  tagScore: number;\n  neighborScore: number;\n  reason: string;\n  suggestedWikilink: string;\n}\n\nconst MAX_CHUNKS = 5000;\nconst SEMANTIC_WEIGHT = 0.5;\nconst TAG_WEIGHT = 0.2;\nconst NEIGHBOR_WEIGHT = 0.3;\n\n// Stop words to ignore when generating tag/label strings\nconst STOP_WORDS = new Set([\n  \"a\", \"an\", \"the\", \"and\", \"or\", \"but\", \"in\", \"on\", \"at\", \"to\", \"for\",\n  \"of\", \"with\", \"by\", \"from\", \"is\", \"it\", \"as\", \"be\", \"was\", \"are\",\n  \"has\", \"had\", \"have\", \"not\", \"this\", \"that\", \"i\", \"my\", \"we\", \"our\",\n]);\n\nfunction extractTagsFromChunkTexts(texts: string[]): Set<string> {\n  const tags = new Set<string>();\n  for (const text of texts) {\n    // Match YAML frontmatter tags block: \"tags:\\n  - tag1\\n  - tag2\"\n    const match = text.match(/^tags:\\s*\\n((?:[ \\t]*-[ \\t]*.+\\n?)*)/m);\n    if (!match) continue;\n    const block = match[1];\n    const lines = block.split(\"\\n\");\n    for (const line of lines) {\n      const tagMatch = line.match(/^[ \\t]*-[ \\t]*(.+)/);\n      if (tagMatch) {\n        const tag = tagMatch[1].trim().toLowerCase();\n        if (tag) tags.add(tag);\n      }\n    }\n  }\n  return tags;\n}\n\nfunction getFileAvgEmbedding(\n  db: Database,\n  projectId: number,\n  path: string,\n): Float32Array | null {\n  const rows = db\n    .prepare(\n      `SELECT embedding FROM memory_chunks\n       WHERE project_id = ? AND path = ? AND embedding IS NOT NULL`,\n    )\n    .all(projectId, path) as Array<{ embedding: Buffer }>;\n\n  if (rows.length === 0) return null;\n\n  const first = deserializeEmbedding(rows[0].embedding);\n  const sum = new Float32Array(first.length);\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    for (let i = 0; i < vec.length; i++) {\n      sum[i] += vec[i];\n    }\n  }\n  const avg = new Float32Array(sum.length);\n  for (let i = 0; i < sum.length; i++) {\n    avg[i] = sum[i] / rows.length;\n  }\n  return avg;\n}\n\nfunction getAllFileEmbeddings(\n  db: Database,\n  projectId: number,\n): Map<string, Float32Array> {\n  const rows = db\n    .prepare(\n      `SELECT path, embedding FROM memory_chunks\n       WHERE project_id = ? AND embedding IS NOT NULL\n       ORDER BY path, start_line\n       LIMIT ?`,\n    )\n    .all(projectId, MAX_CHUNKS) as Array<{ path: string; embedding: Buffer }>;\n\n  const byPath = new Map<string, { sum: Float32Array; count: number }>();\n  for (const row of rows) {\n    const vec = deserializeEmbedding(row.embedding);\n    const entry = byPath.get(row.path);\n    if (!entry) {\n      byPath.set(row.path, { sum: new Float32Array(vec), count: 1 });\n    } else {\n      for (let i = 0; i < vec.length; i++) {\n        entry.sum[i] += vec[i];\n      }\n      entry.count++;\n    }\n  }\n\n  const result = new Map<string, Float32Array>();\n  for (const [path, { sum, count }] of byPath) {\n    const avg = new Float32Array(sum.length);\n    for (let i = 0; i < sum.length; i++) {\n      avg[i] = sum[i] / count;\n    }\n    result.set(path, avg);\n  }\n  return result;\n}\n\nfunction getFileTags(db: Database, projectId: number, path: string): Set<string> {\n  const rows = db\n    .prepare(\n      `SELECT text FROM memory_chunks\n       WHERE project_id = ? AND path = ?\n       ORDER BY start_line\n       LIMIT 5`,\n    )\n    .all(projectId, path) as Array<{ text: string }>;\n  return extractTagsFromChunkTexts(rows.map((r) => r.text));\n}\n\nfunction jaccardSimilarity(a: Set<string>, b: Set<string>): number {\n  if (a.size === 0 && b.size === 0) return 0;\n  let intersection = 0;\n  for (const tag of a) {\n    if (b.has(tag)) intersection++;\n  }\n  const union = a.size + b.size - intersection;\n  return union === 0 ? 0 : intersection / union;\n}\n\nfunction buildReason(\n  semanticScore: number,\n  tagScore: number,\n  neighborScore: number,\n  neighborCount: number,\n): string {\n  const signals: Array<{ label: string; value: number }> = [\n    { label: `Semantically similar (${semanticScore.toFixed(2)})`, value: semanticScore * SEMANTIC_WEIGHT },\n    { label: `Shared tags (${tagScore.toFixed(2)} Jaccard)`, value: tagScore * TAG_WEIGHT },\n    { label: `Linked by ${neighborCount} mutual connection${neighborCount !== 1 ? \"s\" : \"\"}`, value: neighborScore * NEIGHBOR_WEIGHT },\n  ];\n  signals.sort((a, b) => b.value - a.value);\n  return signals[0].label;\n}\n\nfunction suggestedWikilink(vaultPath: string): string {\n  const base = basename(vaultPath);\n  const name = base.endsWith(\".md\") ? base.slice(0, -3) : base;\n  return `[[${name}]]`;\n}\n\n/**\n * Proactively find notes worth linking to a given note, combining semantic similarity,\n * shared tags, and graph-neighborhood signals into a ranked list of suggestions.\n */\nexport async function zettelSuggest(\n  db: Database,\n  opts: SuggestOptions,\n): Promise<Suggestion[]> {\n  const limit = opts.limit ?? 5;\n  const excludeLinked = opts.excludeLinked ?? true;\n\n  // Step 1: get current outbound links\n  const outboundRows = db\n    .prepare(\n      `SELECT target_path FROM vault_links\n       WHERE source_path = ? AND target_path IS NOT NULL`,\n    )\n    .all(opts.notePath) as Array<{ target_path: string }>;\n  const linkedPaths = new Set(outboundRows.map((r) => r.target_path));\n\n  // Step 2: get source embedding\n  const sourceEmbedding = getFileAvgEmbedding(db, opts.vaultProjectId, opts.notePath);\n\n  // Step 3a: get all file-level embeddings for semantic scoring\n  const allEmbeddings = getAllFileEmbeddings(db, opts.vaultProjectId);\n  allEmbeddings.delete(opts.notePath);\n\n  // Step 3b: get source tags\n  const sourceTags = getFileTags(db, opts.vaultProjectId, opts.notePath);\n\n  // Step 3c: compute graph neighborhood (friends-of-friends)\n  const friendTargetRows = db\n    .prepare(\n      `SELECT DISTINCT target_path AS path FROM vault_links\n       WHERE source_path IN (\n         SELECT target_path FROM vault_links\n         WHERE source_path = ? AND target_path IS NOT NULL\n       ) AND target_path IS NOT NULL`,\n    )\n    .all(opts.notePath) as Array<{ path: string }>;\n\n  // For each friend-of-friend, count how many of source's direct friends link to them\n  const friendLinkCounts = new Map<string, number>();\n  for (const { path } of friendTargetRows) {\n    if (path === opts.notePath) continue;\n    friendLinkCounts.set(path, (friendLinkCounts.get(path) ?? 0) + 1);\n  }\n  const maxFriendLinks = Math.max(1, ...friendLinkCounts.values());\n\n  // Get all vault files to enumerate candidates\n  const allFiles = db\n    .prepare(\"SELECT vault_path, title FROM vault_files\")\n    .all() as Array<{ vault_path: string; title: string | null }>;\n\n  const suggestions: Suggestion[] = [];\n\n  for (const { vault_path, title } of allFiles) {\n    if (vault_path === opts.notePath) continue;\n    if (excludeLinked && linkedPaths.has(vault_path)) continue;\n\n    // Semantic score\n    let semanticScore = 0;\n    if (sourceEmbedding) {\n      const candidateEmbedding = allEmbeddings.get(vault_path);\n      if (candidateEmbedding) {\n        semanticScore = Math.max(0, cosineSimilarity(sourceEmbedding, candidateEmbedding));\n      }\n    }\n\n    // Tag score (only compute if candidate might have chunks)\n    let tagScore = 0;\n    if (allEmbeddings.has(vault_path)) {\n      const candidateTags = getFileTags(db, opts.vaultProjectId, vault_path);\n      tagScore = jaccardSimilarity(sourceTags, candidateTags);\n    }\n\n    // Neighbor score\n    const friendCount = friendLinkCounts.get(vault_path) ?? 0;\n    const neighborScore = friendCount / maxFriendLinks;\n\n    const score =\n      SEMANTIC_WEIGHT * semanticScore +\n      TAG_WEIGHT * tagScore +\n      NEIGHBOR_WEIGHT * neighborScore;\n\n    // Only include if there is at least some signal\n    if (score <= 0) continue;\n\n    const reason = buildReason(semanticScore, tagScore, neighborScore, friendCount);\n\n    suggestions.push({\n      path: vault_path,\n      title,\n      score,\n      semanticScore,\n      tagScore,\n      neighborScore,\n      reason,\n      suggestedWikilink: suggestedWikilink(vault_path),\n    });\n  }\n\n  suggestions.sort((a, b) => b.score - a.score);\n  return suggestions.slice(0, 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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@tekmidian/pai",
-  "version": "0.4.0",
+  "version": "0.5.1",
   "description": "PAI Knowledge OS — Personal AI Infrastructure with federated memory and project management",
   "type": "module",
   "main": "dist/index.mjs",