@tekmidian/pai 0.5.7 → 0.6.0

package/dist/indexer-CMPOiY1r.mjs.map

@@ -1 +0,0 @@
-{"version":3,"file":"indexer-CMPOiY1r.mjs","names":[],"sources":["../src/memory/indexer.ts"],"sourcesContent":["/**\n * File indexer for the PAI federation memory engine.\n *\n * Scans project memory/ and Notes/ directories, chunks markdown files, and\n * inserts the resulting chunks into federation.db for BM25 search.\n *\n * Change detection: files whose SHA-256 hash has not changed since the last\n * index run are skipped, keeping incremental re-indexing fast.\n *\n * Phase 2.5: adds embedChunks() for generating vector embeddings on indexed\n * chunks that do not yet have an embedding stored.\n */\n\nimport { createHash } from \"node:crypto\";\nimport { readFileSync, statSync, readdirSync, existsSync } from \"node:fs\";\nimport { join, relative, basename, normalize } from \"node:path\";\nimport { homedir } from \"node:os\";\nimport type { Database } from \"better-sqlite3\";\nimport { chunkMarkdown } from \"./chunker.js\";\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\nexport interface IndexResult {\n  filesProcessed: number;\n  chunksCreated: number;\n  filesSkipped: number;\n}\n\n// ---------------------------------------------------------------------------\n// Tier detection\n// ---------------------------------------------------------------------------\n\n/**\n * Classify a relative file path into one of the four memory tiers.\n *\n * Rules (in priority order):\n *  - MEMORY.md anywhere in memory/  → 'evergreen'\n *  - YYYY-MM-DD.md in memory/       → 'daily'\n *  - anything else in memory/       → 'topic'\n *  - anything in Notes/             → 'session'\n */\nexport function detectTier(\n  relativePath: string,\n): \"evergreen\" | \"daily\" | \"topic\" | \"session\" {\n  // Normalise to forward slashes and strip leading ./\n  const p = relativePath.replace(/\\\\/g, \"/\").replace(/^\\.\\//, \"\");\n\n  // Notes directory → session tier\n  if (p.startsWith(\"Notes/\") || p === \"Notes\") {\n    return \"session\";\n  }\n\n  const fileName = basename(p);\n\n  // MEMORY.md (case-sensitive match) → evergreen\n  if (fileName === \"MEMORY.md\") {\n    return \"evergreen\";\n  }\n\n  // YYYY-MM-DD.md → daily\n  if (/^\\d{4}-\\d{2}-\\d{2}\\.md$/.test(fileName)) {\n    return \"daily\";\n  }\n\n  // Default for memory/ files\n  return \"topic\";\n}\n\n// ---------------------------------------------------------------------------\n// Chunk ID generation\n// ---------------------------------------------------------------------------\n\n/**\n * Generate a deterministic chunk ID from its coordinates.\n * Format: sha256(\"projectId:path:chunkIndex:startLine:endLine\")\n *\n * The chunkIndex (0-based position within the file) is included so that\n * chunks with approximated line numbers (e.g. from splitBySentences) never\n * produce colliding IDs even when multiple chunks share the same startLine/endLine.\n */\nfunction chunkId(\n  projectId: number,\n  path: string,\n  chunkIndex: number,\n  startLine: number,\n  endLine: number,\n): string {\n  return createHash(\"sha256\")\n    .update(`${projectId}:${path}:${chunkIndex}:${startLine}:${endLine}`)\n    .digest(\"hex\");\n}\n\n// ---------------------------------------------------------------------------\n// File hash\n// ---------------------------------------------------------------------------\n\nfunction sha256File(content: string): string {\n  return createHash(\"sha256\").update(content).digest(\"hex\");\n}\n\n// ---------------------------------------------------------------------------\n// Core indexing operations\n// ---------------------------------------------------------------------------\n\n/**\n * Index a single file into the federation database.\n *\n * @returns true if the file was re-indexed (changed or new), false if skipped.\n */\nexport function indexFile(\n  db: Database,\n  projectId: number,\n  rootPath: string,\n  relativePath: string,\n  source: string,\n  tier: string,\n): boolean {\n  const absPath = join(rootPath, relativePath);\n\n  // Read file content\n  let content: string;\n  let stat: ReturnType<typeof statSync>;\n  try {\n    content = readFileSync(absPath, \"utf8\");\n    stat = statSync(absPath);\n  } catch {\n    // File unreadable or missing — skip silently\n    return false;\n  }\n\n  const hash = sha256File(content);\n  const mtime = Math.floor(stat.mtimeMs);\n  const size = stat.size;\n\n  // Check if the file has changed since last index\n  const existing = db\n    .prepare(\n      \"SELECT hash FROM memory_files WHERE project_id = ? AND path = ?\",\n    )\n    .get(projectId, relativePath) as { hash: string } | undefined;\n\n  if (existing?.hash === hash) {\n    // Unchanged — skip\n    return false;\n  }\n\n  // Delete old chunks for this file from both tables\n  const oldChunkIds = db\n    .prepare(\n      \"SELECT id FROM memory_chunks WHERE project_id = ? AND path = ?\",\n    )\n    .all(projectId, relativePath) as Array<{ id: string }>;\n\n  const deleteFts = db.prepare(\"DELETE FROM memory_fts WHERE id = ?\");\n  const deleteChunk = db.prepare(\n    \"DELETE FROM memory_chunks WHERE project_id = ? AND path = ?\",\n  );\n\n  db.transaction(() => {\n    for (const row of oldChunkIds) {\n      deleteFts.run(row.id);\n    }\n    deleteChunk.run(projectId, relativePath);\n  })();\n\n  // Chunk the new content\n  const chunks = chunkMarkdown(content);\n\n  // Insert new chunks into memory_chunks and memory_fts\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 upsertFile = db.prepare(`\n    INSERT INTO memory_files (project_id, path, source, tier, hash, mtime, size)\n    VALUES (?, ?, ?, ?, ?, ?, ?)\n    ON CONFLICT(project_id, path) DO UPDATE SET\n      source = excluded.source,\n      tier   = excluded.tier,\n      hash   = excluded.hash,\n      mtime  = excluded.mtime,\n      size   = excluded.size\n  `);\n\n  const updatedAt = Date.now();\n\n  db.transaction(() => {\n    for (let i = 0; i < chunks.length; i++) {\n      const chunk = chunks[i]!;\n      const id = chunkId(projectId, relativePath, i, chunk.startLine, chunk.endLine);\n      insertChunk.run(\n        id,\n        projectId,\n        source,\n        tier,\n        relativePath,\n        chunk.startLine,\n        chunk.endLine,\n        chunk.hash,\n        chunk.text,\n        updatedAt,\n      );\n      insertFts.run(\n        chunk.text,\n        id,\n        projectId,\n        relativePath,\n        source,\n        tier,\n        chunk.startLine,\n        chunk.endLine,\n      );\n    }\n    upsertFile.run(projectId, relativePath, source, tier, hash, mtime, size);\n  })();\n\n  return true;\n}\n\n// ---------------------------------------------------------------------------\n// Directory walker\n// ---------------------------------------------------------------------------\n\n/**\n * Safety cap: maximum number of .md files collected per project scan.\n * Prevents runaway scans on huge root paths (e.g. home directory).\n * Projects with more files than this are scanned up to the cap only.\n */\nconst MAX_FILES_PER_PROJECT = 5_000;\n\n/**\n * Maximum recursion depth for directory walks.\n * Prevents deep traversal of large directory trees (e.g. development repos).\n * Depth 0 = the given directory itself (no recursion).\n * Value 6 allows: root → subdirs → sub-subdirs → ... up to 6 levels.\n * Sufficient for memory/, Notes/, and typical docs structures.\n */\nconst MAX_WALK_DEPTH = 6;\n\n/**\n * Recursively collect all .md files under a directory.\n * Returns absolute paths. Stops early if the accumulated count hits the cap\n * or if the recursion depth exceeds MAX_WALK_DEPTH.\n *\n * @param dir    Directory to scan.\n * @param acc    Shared accumulator array (mutated in place for early exit).\n * @param cap    Maximum number of files to collect (across all recursive calls).\n * @param depth  Current recursion depth (0 = the initial call).\n */\nfunction walkMdFiles(\n  dir: string,\n  acc?: string[],\n  cap = MAX_FILES_PER_PROJECT,\n  depth = 0,\n): string[] {\n  const results = acc ?? [];\n  if (!existsSync(dir)) return results;\n  if (results.length >= cap) return results;\n  if (depth > MAX_WALK_DEPTH) return results;\n\n  try {\n    for (const entry of readdirSync(dir, { withFileTypes: true })) {\n      if (results.length >= cap) break;\n      if (entry.isSymbolicLink()) continue;\n      // Skip known junk directories at every recursion depth\n      if (ALWAYS_SKIP_DIRS.has(entry.name)) continue;\n      const full = join(dir, entry.name);\n      if (entry.isDirectory()) {\n        walkMdFiles(full, results, cap, depth + 1);\n      } else if (entry.isFile() && entry.name.endsWith(\".md\")) {\n        results.push(full);\n      }\n    }\n  } catch {\n    // Unreadable directory — skip\n  }\n  return results;\n}\n\n/**\n * Directories to ALWAYS skip, at any depth, during any directory walk.\n * These are build artifacts, dependency trees, and VCS internals that\n * should never be indexed regardless of where they appear in the tree.\n */\nconst ALWAYS_SKIP_DIRS = new Set([\n  // Version control\n  \".git\",\n  // Dependency directories (any language)\n  \"node_modules\",\n  \"vendor\",\n  \"Pods\",              // CocoaPods (iOS/macOS)\n  // Build / compile output\n  \"dist\",\n  \"build\",\n  \"out\",\n  \"DerivedData\",       // Xcode\n  \".next\",             // Next.js\n  // Python virtual environments and caches\n  \".venv\",\n  \"venv\",\n  \"__pycache__\",\n  // General caches\n  \".cache\",\n  \".bun\",\n]);\n\n/**\n * Directories to skip when doing a root-level content scan.\n * These are either already handled by dedicated scans or should never be indexed.\n */\nconst ROOT_SCAN_SKIP_DIRS = new Set([\n  \"memory\",\n  \"Notes\",\n  \".claude\",\n  \".DS_Store\",\n  // Everything in ALWAYS_SKIP_DIRS is also excluded at root level\n  ...ALWAYS_SKIP_DIRS,\n]);\n\n/**\n * Additional directories to skip at the content-scan level (first level below root).\n * These are common macOS/Linux home-directory or repo noise directories that are\n * never meaningful as project content.\n */\nconst CONTENT_SCAN_SKIP_DIRS = new Set([\n  // macOS home directory standard folders\n  \"Library\",\n  \"Applications\",\n  \"Music\",\n  \"Movies\",\n  \"Pictures\",\n  \"Desktop\",\n  \"Downloads\",\n  \"Public\",\n  // Common dev noise\n  \"coverage\",\n  // Everything in ALWAYS_SKIP_DIRS is also excluded at this level\n  ...ALWAYS_SKIP_DIRS,\n]);\n\n/**\n * Recursively collect all .md files under rootPath, excluding directories\n * that are already covered by dedicated scans (memory/, Notes/) and\n * common noise directories (.git, node_modules, etc.).\n *\n * Returns absolute paths for files NOT already handled by the specific scanners.\n * Stops collecting once MAX_FILES_PER_PROJECT is reached.\n */\nfunction walkContentFiles(rootPath: string): string[] {\n  if (!existsSync(rootPath)) return [];\n\n  const results: string[] = [];\n  try {\n    for (const entry of readdirSync(rootPath, { withFileTypes: true })) {\n      if (results.length >= MAX_FILES_PER_PROJECT) break;\n      if (entry.isSymbolicLink()) continue;\n      if (ROOT_SCAN_SKIP_DIRS.has(entry.name)) continue;\n      if (CONTENT_SCAN_SKIP_DIRS.has(entry.name)) continue;\n\n      const full = join(rootPath, entry.name);\n      if (entry.isDirectory()) {\n        walkMdFiles(full, results, MAX_FILES_PER_PROJECT);\n      } else if (entry.isFile() && entry.name.endsWith(\".md\")) {\n        // Skip root-level MEMORY.md — handled by the dedicated evergreen scan\n        if (entry.name !== \"MEMORY.md\") {\n          results.push(full);\n        }\n      }\n    }\n  } catch {\n    // Unreadable directory — skip\n  }\n  return results;\n}\n\n// ---------------------------------------------------------------------------\n// Project-level indexing\n// ---------------------------------------------------------------------------\n\n/**\n * Index all memory, Notes, and content files for a single registered project.\n *\n * Scans:\n *  - {rootPath}/MEMORY.md    → source='memory', tier='evergreen'\n *  - {rootPath}/memory/      → source='memory', tier from detectTier()\n *  - {rootPath}/Notes/       → source='notes',  tier='session'\n *  - {rootPath}/**\\/\\*.md    → source='content', tier='topic'  (all other .md files, recursive)\n *  - {claudeNotesDir}/       → source='notes',  tier='session'  (if set and different)\n *\n * The content scan covers projects like job-discussions where markdown files\n * live in date/topic subdirectories rather than a memory/ folder.  The\n * memory/, Notes/, .git/, and node_modules/ directories are excluded from\n * the content scan to avoid double-indexing.\n *\n * The claudeNotesDir parameter points to ~/.claude/projects/{encoded}/Notes/\n * where Claude Code writes session notes for a given working directory.\n * It is stored on the project row as claude_notes_dir after a registry scan.\n */\n/**\n * Number of files to process before yielding to the event loop inside\n * indexProject. Keeps IPC responsive even while indexing large projects.\n * Lower = more responsive but more overhead. 10 is a good balance.\n */\nconst INDEX_YIELD_EVERY = 10;\n\n/**\n * Returns true if rootPath should skip the recursive content scan.\n *\n * Skips content scanning for:\n *  - The home directory itself or any ancestor (too broad — millions of files)\n *  - Git repositories (code repos — index memory/ and Notes/ only, not all .md files)\n *\n * The content scan is still useful for Obsidian vaults, Notes folders, and\n * other doc-centric project trees where ALL markdown files are meaningful.\n *\n * The memory/, Notes/, and claude_notes_dir scans always run regardless.\n */\nfunction isPathTooBroadForContentScan(rootPath: string): boolean {\n  const normalized = normalize(rootPath);\n  const home = homedir();\n\n  // Skip the home directory itself or any ancestor of home\n  if (home.startsWith(normalized) || normalized === \"/\") {\n    return true;\n  }\n\n  // Skip home directory itself (depth 0)\n  if (normalized.startsWith(home)) {\n    const rel = normalized.slice(home.length).replace(/^\\//, \"\");\n    const depth = rel ? rel.split(\"/\").length : 0;\n    if (depth === 0) return true;\n  }\n\n  // Skip git repositories — content scan is only for doc-centric projects\n  // (Obsidian vaults, knowledge bases). Code repos use memory/ and Notes/ only.\n  if (existsSync(join(normalized, \".git\"))) {\n    return true;\n  }\n\n  return false;\n}\n\nexport async function indexProject(\n  db: Database,\n  projectId: number,\n  rootPath: string,\n  claudeNotesDir?: string | null,\n): Promise<IndexResult> {\n  const result: IndexResult = {\n    filesProcessed: 0,\n    chunksCreated: 0,\n    filesSkipped: 0,\n  };\n\n  const filesToIndex: Array<{ absPath: string; rootBase: string; source: string; tier: string }> = [];\n\n  // Root-level MEMORY.md\n  const rootMemoryMd = join(rootPath, \"MEMORY.md\");\n  if (existsSync(rootMemoryMd)) {\n    filesToIndex.push({ absPath: rootMemoryMd, rootBase: rootPath, source: \"memory\", tier: \"evergreen\" });\n  }\n\n  // memory/ directory\n  const memoryDir = join(rootPath, \"memory\");\n  for (const absPath of walkMdFiles(memoryDir)) {\n    const relPath = relative(rootPath, absPath);\n    const tier = detectTier(relPath);\n    filesToIndex.push({ absPath, rootBase: rootPath, source: \"memory\", tier });\n  }\n\n  // {rootPath}/Notes/ directory\n  const notesDir = join(rootPath, \"Notes\");\n  for (const absPath of walkMdFiles(notesDir)) {\n    filesToIndex.push({ absPath, rootBase: rootPath, source: \"notes\", tier: \"session\" });\n  }\n\n  // Synthetic session-title chunks for Notes files with the standard filename format:\n  // \"NNNN - YYYY-MM-DD - Descriptive Title.md\"\n  // These are small, high-signal chunks that make session titles searchable via BM25 and embeddings.\n  {\n    const SESSION_TITLE_RE = /^(\\d{4})\\s*-\\s*(\\d{4}-\\d{2}-\\d{2})\\s*-\\s*(.+)\\.md$/;\n    const titleInsertChunk = db.prepare(`\n      INSERT OR IGNORE INTO memory_chunks (id, project_id, source, tier, path, start_line, end_line, hash, text, updated_at)\n      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n    `);\n    const titleInsertFts = db.prepare(`\n      INSERT OR IGNORE INTO memory_fts (text, id, project_id, path, source, tier, start_line, end_line)\n      VALUES (?, ?, ?, ?, ?, ?, ?, ?)\n    `);\n    const updatedAt = Date.now();\n    for (const absPath of walkMdFiles(notesDir)) {\n      const fileName = basename(absPath);\n      const m = SESSION_TITLE_RE.exec(fileName);\n      if (!m) continue;\n      const [, num, date, title] = m;\n      const text = `Session #${num} ${date}: ${title}`;\n      const relPath = relative(rootPath, absPath);\n      const syntheticPath = `${relPath}::title`;\n      const id = chunkId(projectId, syntheticPath, 0, 0, 0);\n      const hash = sha256File(text);\n      db.transaction(() => {\n        titleInsertChunk.run(id, projectId, \"notes\", \"session\", syntheticPath, 0, 0, hash, text, updatedAt);\n        titleInsertFts.run(text, id, projectId, syntheticPath, \"notes\", \"session\", 0, 0);\n      })();\n    }\n  }\n\n  // {rootPath}/**/*.md — all other markdown content (e.g. year/month/topic dirs)\n  // Uses walkContentFiles which skips memory/, Notes/, .git/, node_modules/ etc.\n  // Skip the content scan for paths that are too broad (home dir, filesystem root, etc.)\n  // to avoid runaway directory traversal. Memory and Notes scans above are always safe\n  // because they target specific named subdirectories.\n  if (!isPathTooBroadForContentScan(rootPath)) {\n    for (const absPath of walkContentFiles(rootPath)) {\n      filesToIndex.push({ absPath, rootBase: rootPath, source: \"content\", tier: \"topic\" });\n    }\n  }\n\n  // Claude Code session notes directory (~/.claude/projects/{encoded}/Notes/)\n  // Only scan if it is set, exists, and is not the same path as rootPath/Notes/\n  if (claudeNotesDir && claudeNotesDir !== notesDir) {\n    for (const absPath of walkMdFiles(claudeNotesDir)) {\n      filesToIndex.push({ absPath, rootBase: claudeNotesDir, source: \"notes\", tier: \"session\" });\n    }\n\n    // Synthetic title chunks for claude notes dir\n    {\n      const SESSION_TITLE_RE_CLAUDE = /^(\\d{4})\\s*-\\s*(\\d{4}-\\d{2}-\\d{2})\\s*-\\s*(.+)\\.md$/;\n      const updatedAt = Date.now();\n      const titleInsertChunk2 = db.prepare(`\n        INSERT OR IGNORE INTO memory_chunks (id, project_id, source, tier, path, start_line, end_line, hash, text, updated_at)\n        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n      `);\n      const titleInsertFts2 = db.prepare(`\n        INSERT OR IGNORE INTO memory_fts (text, id, project_id, path, source, tier, start_line, end_line)\n        VALUES (?, ?, ?, ?, ?, ?, ?, ?)\n      `);\n      for (const absPath of walkMdFiles(claudeNotesDir)) {\n        const fileName = basename(absPath);\n        const m = SESSION_TITLE_RE_CLAUDE.exec(fileName);\n        if (!m) continue;\n        const [, num, date, title] = m;\n        const text = `Session #${num} ${date}: ${title}`;\n        const relPath = relative(claudeNotesDir, absPath);\n        const syntheticPath = `${relPath}::title`;\n        const id = chunkId(projectId, syntheticPath, 0, 0, 0);\n        const hash = sha256File(text);\n        db.transaction(() => {\n          titleInsertChunk2.run(id, projectId, \"notes\", \"session\", syntheticPath, 0, 0, hash, text, updatedAt);\n          titleInsertFts2.run(text, id, projectId, syntheticPath, \"notes\", \"session\", 0, 0);\n        })();\n      }\n    }\n\n    // Derive the sibling memory/ directory: .../Notes/ → .../memory/\n    if (claudeNotesDir.endsWith(\"/Notes\")) {\n      const claudeProjectDir = claudeNotesDir.slice(0, -\"/Notes\".length);\n      const claudeMemoryDir = join(claudeProjectDir, \"memory\");\n\n      // MEMORY.md at the Claude Code project dir level (sibling of Notes/)\n      const claudeMemoryMd = join(claudeProjectDir, \"MEMORY.md\");\n      if (existsSync(claudeMemoryMd)) {\n        filesToIndex.push({\n          absPath: claudeMemoryMd,\n          rootBase: claudeProjectDir,\n          source: \"memory\",\n          tier: \"evergreen\",\n        });\n      }\n\n      // memory/ directory sibling of Notes/\n      for (const absPath of walkMdFiles(claudeMemoryDir)) {\n        const relPath = relative(claudeProjectDir, absPath);\n        const tier = detectTier(relPath);\n        filesToIndex.push({ absPath, rootBase: claudeProjectDir, source: \"memory\", tier });\n      }\n    }\n  }\n\n  // Yield after collection phase (which is synchronous) before we start processing\n  await yieldToEventLoop();\n\n  let filesSinceYield = 0;\n\n  for (const { absPath, rootBase, source, tier } of filesToIndex) {\n    // Yield to the event loop periodically so the IPC server stays responsive\n    if (filesSinceYield >= INDEX_YIELD_EVERY) {\n      await yieldToEventLoop();\n      filesSinceYield = 0;\n    }\n    filesSinceYield++;\n\n    const relPath = relative(rootBase, absPath);\n    const changed = indexFile(db, projectId, rootBase, relPath, source, tier);\n\n    if (changed) {\n      // Count chunks created for this file\n      const count = db\n        .prepare(\n          \"SELECT COUNT(*) as n FROM memory_chunks WHERE project_id = ? AND path = ?\",\n        )\n        .get(projectId, relPath) as { n: number };\n\n      result.filesProcessed++;\n      result.chunksCreated += count.n;\n    } else {\n      result.filesSkipped++;\n    }\n  }\n\n  // ---------------------------------------------------------------------------\n  // Prune stale paths: remove DB entries for files that no longer exist on disk.\n  // This handles renames, moves, and deletions — the indexer only adds/updates,\n  // so without pruning, old paths accumulate forever.\n  // ---------------------------------------------------------------------------\n\n  const livePaths = new Set<string>();\n  for (const { absPath, rootBase } of filesToIndex) {\n    livePaths.add(relative(rootBase, absPath));\n  }\n\n  // Query all distinct paths in memory_chunks for this project\n  const dbChunkPaths = db\n    .prepare(\"SELECT DISTINCT path FROM memory_chunks WHERE project_id = ?\")\n    .all(projectId) as Array<{ path: string }>;\n\n  const stalePaths: string[] = [];\n  for (const row of dbChunkPaths) {\n    // Synthetic title paths (ending in \"::title\") are live if their base file is live\n    const basePath = row.path.endsWith(\"::title\")\n      ? row.path.slice(0, -\"::title\".length)\n      : row.path;\n    if (!livePaths.has(basePath)) {\n      stalePaths.push(row.path);\n    }\n  }\n\n  if (stalePaths.length > 0) {\n    const deleteChunksFts = db.prepare(\"DELETE FROM memory_fts WHERE id = ?\");\n    const deleteChunks = db.prepare(\n      \"DELETE FROM memory_chunks WHERE project_id = ? AND path = ?\",\n    );\n    const deleteFile = db.prepare(\n      \"DELETE FROM memory_files WHERE project_id = ? AND path = ?\",\n    );\n\n    db.transaction(() => {\n      for (const stalePath of stalePaths) {\n        const chunkIds = db\n          .prepare(\"SELECT id FROM memory_chunks WHERE project_id = ? AND path = ?\")\n          .all(projectId, stalePath) as Array<{ id: string }>;\n        for (const { id } of chunkIds) {\n          deleteChunksFts.run(id);\n        }\n        deleteChunks.run(projectId, stalePath);\n        deleteFile.run(projectId, stalePath);\n      }\n    })();\n  }\n\n  return result;\n}\n\n// ---------------------------------------------------------------------------\n// Global indexing (all registered projects)\n// ---------------------------------------------------------------------------\n\n/**\n * Yield to the Node.js event loop between projects so the IPC server\n * remains responsive during long index runs.\n */\nfunction yieldToEventLoop(): Promise<void> {\n  return new Promise((resolve) => setImmediate(resolve));\n}\n\n/**\n * Index all active projects registered in the registry DB.\n *\n * Async: yields to the event loop between each project so that the daemon's\n * Unix socket server can process IPC requests (e.g. status) while indexing.\n */\nexport async function indexAll(\n  db: Database,\n  registryDb: Database,\n): Promise<{ projects: number; result: IndexResult }> {\n  const projects = registryDb\n    .prepare(\"SELECT id, root_path, claude_notes_dir FROM projects WHERE status = 'active'\")\n    .all() as Array<{ id: number; root_path: string; claude_notes_dir: string | null }>;\n\n  const totals: IndexResult = {\n    filesProcessed: 0,\n    chunksCreated: 0,\n    filesSkipped: 0,\n  };\n\n  for (const project of projects) {\n    // Yield before each project so the event loop can drain IPC requests\n    await yieldToEventLoop();\n\n    const r = await indexProject(db, project.id, project.root_path, project.claude_notes_dir);\n    totals.filesProcessed += r.filesProcessed;\n    totals.chunksCreated += r.chunksCreated;\n    totals.filesSkipped += r.filesSkipped;\n  }\n\n  return { projects: projects.length, result: totals };\n}\n\n// ---------------------------------------------------------------------------\n// Embedding generation\n// ---------------------------------------------------------------------------\n\nexport interface EmbedResult {\n  chunksEmbedded: number;\n  chunksSkipped: number;\n}\n\n/**\n * Generate and store embeddings for chunks that do not yet have one.\n *\n * Because better-sqlite3 is synchronous but the embedding pipeline is async,\n * we fetch all unembedded chunk texts first, generate embeddings in batches,\n * and then write them back in a transaction.\n *\n * @param db         Open federation database.\n * @param projectId  Optional — restrict to a specific project.\n * @param batchSize  Number of chunks to embed per round. Default 50.\n * @param onProgress Optional callback called after each batch with running totals.\n */\nexport async function embedChunks(\n  db: Database,\n  projectId?: number,\n  batchSize = 50,\n  onProgress?: (embedded: number, total: number) => void,\n): Promise<EmbedResult> {\n  // Dynamic import — keeps the heavy ML runtime out of the module load path\n  const { generateEmbedding, serializeEmbedding } = await import(\"./embeddings.js\");\n\n  const conditions = [\"embedding IS NULL\"];\n  const params: (string | number)[] = [];\n\n  if (projectId !== undefined) {\n    conditions.push(\"project_id = ?\");\n    params.push(projectId);\n  }\n\n  const where = \"WHERE \" + conditions.join(\" AND \");\n\n  const rows = db\n    .prepare(`SELECT id, text FROM memory_chunks ${where} ORDER BY id`)\n    .all(...params) as Array<{ id: string; text: string }>;\n\n  if (rows.length === 0) {\n    return { chunksEmbedded: 0, chunksSkipped: 0 };\n  }\n\n  const updateStmt = db.prepare(\n    \"UPDATE memory_chunks SET embedding = ? 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package/dist/indexer-backend-CIMXedqk.mjs.map

@@ -1 +0,0 @@
-{"version":3,"file":"indexer-backend-CIMXedqk.mjs","names":[],"sources":["../src/memory/indexer-backend.ts"],"sourcesContent":["/**\n * Backend-aware indexer for PAI federation memory.\n *\n * This module provides the same functionality as indexer.ts but writes\n * through the StorageBackend interface instead of directly to better-sqlite3.\n * Used when the daemon is configured with the Postgres backend.\n *\n * The SQLite path still uses indexer.ts directly (which is faster for SQLite\n * due to synchronous transactions).\n */\n\nimport { createHash } from \"node:crypto\";\nimport { readFileSync, statSync, readdirSync, existsSync } from \"node:fs\";\nimport { join, relative, basename, normalize } from \"node:path\";\n\n// ---------------------------------------------------------------------------\n// Session title parsing\n// ---------------------------------------------------------------------------\n\nconst SESSION_TITLE_RE = /^(\\d{4})\\s*-\\s*(\\d{4}-\\d{2}-\\d{2})\\s*-\\s*(.+)\\.md$/;\n\n/**\n * Parse a session title from a Notes filename.\n * Format: \"NNNN - YYYY-MM-DD - Descriptive Title.md\"\n * Returns a synthetic chunk text like \"Session #0086 2026-02-23: Pai Daemon Background Service\"\n * or null if the filename doesn't match the expected pattern.\n */\nexport function parseSessionTitleChunk(fileName: string): string | null {\n  const m = SESSION_TITLE_RE.exec(fileName);\n  if (!m) return null;\n  const [, num, date, title] = m;\n  return `Session #${num} ${date}: ${title}`;\n}\nimport { homedir } from \"node:os\";\nimport type { Database } from \"better-sqlite3\";\nimport type { StorageBackend, ChunkRow } from \"../storage/interface.js\";\nimport type { IndexResult } from \"./indexer.js\";\nimport { chunkMarkdown } from \"./chunker.js\";\nimport { detectTier } from \"./indexer.js\";\n\n// ---------------------------------------------------------------------------\n// Constants (mirrored from indexer.ts)\n// ---------------------------------------------------------------------------\n\nconst MAX_FILES_PER_PROJECT = 5_000;\nconst MAX_WALK_DEPTH = 6;\nconst INDEX_YIELD_EVERY = 10;\n\n/**\n * Directories to ALWAYS skip, at any depth, during any directory walk.\n * These are build artifacts, dependency trees, and VCS internals that\n * should never be indexed regardless of where they appear in the tree.\n */\nconst ALWAYS_SKIP_DIRS = new Set([\n  // Version control\n  \".git\",\n  // Dependency directories (any language)\n  \"node_modules\",\n  \"vendor\",\n  \"Pods\",              // CocoaPods (iOS/macOS)\n  // Build / compile output\n  \"dist\",\n  \"build\",\n  \"out\",\n  \"DerivedData\",       // Xcode\n  \".next\",             // Next.js\n  // Python virtual environments and caches\n  \".venv\",\n  \"venv\",\n  \"__pycache__\",\n  // General caches\n  \".cache\",\n  \".bun\",\n]);\n\nconst ROOT_SCAN_SKIP_DIRS = new Set([\n  \"memory\", \"Notes\", \".claude\", \".DS_Store\",\n  ...ALWAYS_SKIP_DIRS,\n]);\n\nconst CONTENT_SCAN_SKIP_DIRS = new Set([\n  \"Library\", \"Applications\", \"Music\", \"Movies\", \"Pictures\", \"Desktop\",\n  \"Downloads\", \"Public\", \"coverage\",\n  ...ALWAYS_SKIP_DIRS,\n]);\n\n// ---------------------------------------------------------------------------\n// Helpers (same logic as indexer.ts)\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 walkMdFiles(\n  dir: string,\n  acc?: string[],\n  cap = MAX_FILES_PER_PROJECT,\n  depth = 0,\n): string[] {\n  const results = acc ?? [];\n  if (!existsSync(dir)) return results;\n  if (results.length >= cap) return results;\n  if (depth > MAX_WALK_DEPTH) return results;\n  try {\n    for (const entry of readdirSync(dir, { withFileTypes: true })) {\n      if (results.length >= cap) break;\n      if (entry.isSymbolicLink()) continue;\n      // Skip known junk directories at every recursion depth\n      if (ALWAYS_SKIP_DIRS.has(entry.name)) continue;\n      const full = join(dir, entry.name);\n      if (entry.isDirectory()) {\n        walkMdFiles(full, results, cap, depth + 1);\n      } else if (entry.isFile() && entry.name.endsWith(\".md\")) {\n        results.push(full);\n      }\n    }\n  } catch { /* skip unreadable */ }\n  return results;\n}\n\nfunction walkContentFiles(rootPath: string): string[] {\n  if (!existsSync(rootPath)) return [];\n  const results: string[] = [];\n  try {\n    for (const entry of readdirSync(rootPath, { withFileTypes: true })) {\n      if (results.length >= MAX_FILES_PER_PROJECT) break;\n      if (entry.isSymbolicLink()) continue;\n      if (ROOT_SCAN_SKIP_DIRS.has(entry.name)) continue;\n      if (CONTENT_SCAN_SKIP_DIRS.has(entry.name)) continue;\n      const full = join(rootPath, entry.name);\n      if (entry.isDirectory()) {\n        walkMdFiles(full, results, MAX_FILES_PER_PROJECT);\n      } else if (entry.isFile() && entry.name.endsWith(\".md\")) {\n        if (entry.name !== \"MEMORY.md\") results.push(full);\n      }\n    }\n  } catch { /* skip */ }\n  return results;\n}\n\nfunction isPathTooBroadForContentScan(rootPath: string): boolean {\n  const normalized = normalize(rootPath);\n  const home = homedir();\n  if (home.startsWith(normalized) || normalized === \"/\") return true;\n  if (normalized.startsWith(home)) {\n    const rel = normalized.slice(home.length).replace(/^\\//, \"\");\n    const depth = rel ? rel.split(\"/\").length : 0;\n    if (depth === 0) return true;\n  }\n  if (existsSync(join(normalized, \".git\"))) return true;\n  return false;\n}\n\nfunction yieldToEventLoop(): Promise<void> {\n  return new Promise((resolve) => setImmediate(resolve));\n}\n\n// ---------------------------------------------------------------------------\n// File indexing via StorageBackend\n// ---------------------------------------------------------------------------\n\n/**\n * Index a single file through the StorageBackend interface.\n * Returns true if the file was re-indexed (changed or new), false if skipped.\n */\nexport async function indexFileWithBackend(\n  backend: StorageBackend,\n  projectId: number,\n  rootPath: string,\n  relativePath: string,\n  source: string,\n  tier: string,\n): Promise<boolean> {\n  const absPath = join(rootPath, relativePath);\n\n  let content: string;\n  let stat: ReturnType<typeof statSync>;\n  try {\n    content = readFileSync(absPath, \"utf8\");\n    stat = statSync(absPath);\n  } catch {\n    return false;\n  }\n\n  const hash = sha256File(content);\n  const mtime = Math.floor(stat.mtimeMs);\n  const size = stat.size;\n\n  // Change detection\n  const existingHash = await backend.getFileHash(projectId, relativePath);\n  if (existingHash === hash) return false;\n\n  // Delete old chunks\n  await backend.deleteChunksForFile(projectId, relativePath);\n\n  // Chunk the content\n  const rawChunks = chunkMarkdown(content);\n  const updatedAt = Date.now();\n\n  const chunks: ChunkRow[] = rawChunks.map((c, i) => ({\n    id: chunkId(projectId, relativePath, i, c.startLine, c.endLine),\n    projectId,\n    source,\n    tier,\n    path: relativePath,\n    startLine: c.startLine,\n    endLine: c.endLine,\n    hash: c.hash,\n    text: c.text,\n    updatedAt,\n    embedding: null,\n  }));\n\n  // Insert chunks + update file record\n  await backend.insertChunks(chunks);\n  await backend.upsertFile({ projectId, path: relativePath, source, tier, hash, mtime, size });\n\n  return true;\n}\n\n// ---------------------------------------------------------------------------\n// Project-level indexing via StorageBackend\n// ---------------------------------------------------------------------------\n\nexport async function indexProjectWithBackend(\n  backend: StorageBackend,\n  projectId: number,\n  rootPath: string,\n  claudeNotesDir?: string | null,\n): Promise<IndexResult> {\n  const result: IndexResult = { filesProcessed: 0, chunksCreated: 0, filesSkipped: 0 };\n\n  const filesToIndex: Array<{ absPath: string; rootBase: string; source: string; tier: string }> = [];\n\n  const rootMemoryMd = join(rootPath, \"MEMORY.md\");\n  if (existsSync(rootMemoryMd)) {\n    filesToIndex.push({ absPath: rootMemoryMd, rootBase: rootPath, source: \"memory\", tier: \"evergreen\" });\n  }\n\n  const memoryDir = join(rootPath, \"memory\");\n  for (const absPath of walkMdFiles(memoryDir)) {\n    const relPath = relative(rootPath, absPath);\n    const tier = detectTier(relPath);\n    filesToIndex.push({ absPath, rootBase: rootPath, source: \"memory\", tier });\n  }\n\n  const notesDir = join(rootPath, \"Notes\");\n  for (const absPath of walkMdFiles(notesDir)) {\n    filesToIndex.push({ absPath, rootBase: rootPath, source: \"notes\", tier: \"session\" });\n  }\n\n  // Synthetic session-title chunks: parse titles from Notes filenames and insert\n  // as high-signal chunks so session names are searchable via BM25 and embeddings.\n  {\n    const updatedAt = Date.now();\n    for (const absPath of walkMdFiles(notesDir)) {\n      const fileName = basename(absPath);\n      const text = parseSessionTitleChunk(fileName);\n      if (!text) continue;\n      const relPath = relative(rootPath, absPath);\n      const syntheticPath = `${relPath}::title`;\n      const id = chunkId(projectId, syntheticPath, 0, 0, 0);\n      const hash = sha256File(text);\n      const titleChunk: import(\"../storage/interface.js\").ChunkRow = {\n        id, projectId, source: \"notes\", tier: \"session\",\n        path: syntheticPath, startLine: 0, endLine: 0,\n        hash, text, updatedAt, embedding: null,\n      };\n      try {\n        await backend.insertChunks([titleChunk]);\n      } catch {\n        // Skip title chunks that cause backend errors\n      }\n    }\n  }\n\n  if (!isPathTooBroadForContentScan(rootPath)) {\n    for (const absPath of walkContentFiles(rootPath)) {\n      filesToIndex.push({ absPath, rootBase: rootPath, source: \"content\", tier: \"topic\" });\n    }\n  }\n\n  if (claudeNotesDir && claudeNotesDir !== notesDir) {\n    for (const absPath of walkMdFiles(claudeNotesDir)) {\n      filesToIndex.push({ absPath, rootBase: claudeNotesDir, source: \"notes\", tier: \"session\" });\n    }\n\n    // Synthetic title chunks for claude notes dir\n    {\n      const updatedAt = Date.now();\n      for (const absPath of walkMdFiles(claudeNotesDir)) {\n        const fileName = basename(absPath);\n        const text = parseSessionTitleChunk(fileName);\n        if (!text) continue;\n        const relPath = relative(claudeNotesDir, absPath);\n        const syntheticPath = `${relPath}::title`;\n        const id = chunkId(projectId, syntheticPath, 0, 0, 0);\n        const hash = sha256File(text);\n        const titleChunk: import(\"../storage/interface.js\").ChunkRow = {\n          id, projectId, source: \"notes\", tier: \"session\",\n          path: syntheticPath, startLine: 0, endLine: 0,\n          hash, text, updatedAt, embedding: null,\n        };\n        try {\n          await backend.insertChunks([titleChunk]);\n        } catch {\n          // Skip title chunks that cause backend errors\n        }\n      }\n    }\n\n    if (claudeNotesDir.endsWith(\"/Notes\")) {\n      const claudeProjectDir = claudeNotesDir.slice(0, -\"/Notes\".length);\n      const claudeMemoryMd = join(claudeProjectDir, \"MEMORY.md\");\n      if (existsSync(claudeMemoryMd)) {\n        filesToIndex.push({ absPath: claudeMemoryMd, rootBase: claudeProjectDir, source: \"memory\", tier: \"evergreen\" });\n      }\n      const claudeMemoryDir = join(claudeProjectDir, \"memory\");\n      for (const absPath of walkMdFiles(claudeMemoryDir)) {\n        const relPath = relative(claudeProjectDir, absPath);\n        const tier = detectTier(relPath);\n        filesToIndex.push({ absPath, rootBase: claudeProjectDir, source: \"memory\", tier });\n      }\n    }\n  }\n\n  await yieldToEventLoop();\n\n  let filesSinceYield = 0;\n\n  for (const { absPath, rootBase, source, tier } of filesToIndex) {\n    if (filesSinceYield >= INDEX_YIELD_EVERY) {\n      await yieldToEventLoop();\n      filesSinceYield = 0;\n    }\n    filesSinceYield++;\n\n    const relPath = relative(rootBase, absPath);\n    try {\n      const changed = await indexFileWithBackend(backend, projectId, rootBase, relPath, source, tier);\n\n      if (changed) {\n        // Count chunks — we know we just inserted them, count from the chunk IDs\n        const ids = await backend.getChunkIds(projectId, relPath);\n        result.filesProcessed++;\n        result.chunksCreated += ids.length;\n      } else {\n        result.filesSkipped++;\n      }\n    } catch {\n      // Skip files that cause backend errors (e.g. null bytes in Postgres)\n      result.filesSkipped++;\n    }\n  }\n\n  // ---------------------------------------------------------------------------\n  // Prune stale paths: remove DB entries for files that no longer exist on disk.\n  // This handles renames, moves, and deletions — the indexer only adds/updates,\n  // so without pruning, old paths accumulate forever.\n  // ---------------------------------------------------------------------------\n\n  const livePaths = new Set<string>();\n  for (const { absPath, rootBase } of filesToIndex) {\n    livePaths.add(relative(rootBase, absPath));\n  }\n\n  const dbChunkPaths = await backend.getDistinctChunkPaths(projectId);\n\n  const stalePaths: string[] = [];\n  for (const p of dbChunkPaths) {\n    const basePath = p.endsWith(\"::title\") ? p.slice(0, -\"::title\".length) : p;\n    if (!livePaths.has(basePath)) {\n      stalePaths.push(p);\n    }\n  }\n\n  if (stalePaths.length > 0) {\n    await backend.deletePaths(projectId, stalePaths);\n  }\n\n  return result;\n}\n\n// ---------------------------------------------------------------------------\n// Embedding generation via StorageBackend\n// ---------------------------------------------------------------------------\n\nconst EMBED_BATCH_SIZE = 50;\nconst EMBED_YIELD_EVERY = 10;\n\n/**\n * Generate and store embeddings for all unembedded chunks via the StorageBackend.\n *\n * Processes chunks in batches of EMBED_BATCH_SIZE, yielding to the event loop\n * every EMBED_YIELD_EVERY chunks to avoid blocking IPC calls from MCP shims.\n *\n * The optional `shouldStop` callback is checked between every batch. When it\n * returns true the embed loop exits early so the caller (e.g. the daemon\n * shutdown handler) can close the pool without racing against active queries.\n *\n * Returns the number of newly embedded chunks.\n */\nexport async function embedChunksWithBackend(\n  backend: StorageBackend,\n  shouldStop?: () => boolean,\n): Promise<number> {\n  const { generateEmbedding, serializeEmbedding } = await import(\"./embeddings.js\");\n\n  const rows = await backend.getUnembeddedChunkIds();\n  if (rows.length === 0) return 0;\n\n  const total = rows.length;\n  let embedded = 0;\n\n  for (let i = 0; i < rows.length; i += EMBED_BATCH_SIZE) {\n    // Check cancellation between every batch before touching the pool again\n    if (shouldStop?.()) {\n      process.stderr.write(\n        `[pai-daemon] Embed pass cancelled after ${embedded}/${total} chunks (shutdown requested)\\n`\n      );\n      break;\n    }\n\n    const batch = rows.slice(i, i + EMBED_BATCH_SIZE);\n\n    for (let j = 0; j < batch.length; j++) {\n      const { id, text } = batch[j];\n\n      // Yield to the event loop periodically to keep IPC responsive\n      if ((embedded + j) % EMBED_YIELD_EVERY === 0) {\n        await yieldToEventLoop();\n      }\n\n      const vec = await generateEmbedding(text);\n      const blob = serializeEmbedding(vec);\n      await backend.updateEmbedding(id, blob);\n    }\n\n    embedded += batch.length;\n    process.stderr.write(\n      `[pai-daemon] Embedded ${embedded}/${total} chunks\\n`\n    );\n  }\n\n  return embedded;\n}\n\n// ---------------------------------------------------------------------------\n// Global indexing via StorageBackend\n// ---------------------------------------------------------------------------\n\nexport async function indexAllWithBackend(\n  backend: StorageBackend,\n  registryDb: Database,\n): Promise<{ projects: number; result: IndexResult }> {\n  const projects = registryDb\n    .prepare(\"SELECT id, root_path, claude_notes_dir FROM projects WHERE status = 'active'\")\n    .all() as Array<{ id: number; root_path: string; claude_notes_dir: string | null }>;\n\n  const totals: IndexResult = { filesProcessed: 0, chunksCreated: 0, filesSkipped: 0 };\n\n  for (const project of projects) {\n    await yieldToEventLoop();\n    const r = await indexProjectWithBackend(backend, project.id, project.root_path, project.claude_notes_dir);\n    totals.filesProcessed += r.filesProcessed;\n    totals.chunksCreated += r.chunksCreated;\n    totals.filesSkipped += r.filesSkipped;\n  }\n\n  return { projects: projects.length, result: totals 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package/dist/mcp/index.d.mts

@@ -1 +0,0 @@
-export { };

package/dist/mcp/index.mjs

@@ -1,500 +0,0 @@
-#!/usr/bin/env node
-import { n as openRegistry } from "../db-BtuN768f.mjs";
-import { n as openFederation } from "../db-Dp8VXIMR.mjs";
-import "../embeddings-DGRAPAYb.mjs";
-import "../search-_oHfguA5.mjs";
-import { a as record, i as number, n as array, o as string, r as boolean, s as unknown, t as _enum } from "../schemas-BFIgGntb.mjs";
-import { o as loadConfig } from "../config-Cf92lGX_.mjs";
-import { _ as toolZettelSurprise, a as toolProjectHealth, d as toolSessionRoute, f as toolTopicDetect, g as toolZettelSuggest, h as toolZettelHealth, i as toolProjectDetect, l as toolRegistrySearch, m as toolZettelExplore, n as toolMemorySearch, o as toolProjectInfo, p as toolZettelConverse, r as toolNotificationConfig, s as toolProjectList, t as toolMemoryGet, u as toolSessionList, v as toolZettelThemes } from "../tools-DV_lsiCc.mjs";
-import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
-
-//#region src/mcp/server.ts
-/**
-* PAI Knowledge OS — MCP Server (Phase 3)
-*
-* Exposes PAI registry and memory as MCP tools callable by Claude Code.
-*
-* Tools:
-*   memory_search   — BM25 search across indexed memory/notes
-*   memory_get      — Read a specific file or lines from a project
-*   project_info    — Get details for a project (by slug or current dir)
-*   project_list    — List projects with optional filters
-*   session_list    — List sessions for a project
-*   registry_search — Full-text search over project slugs/names/paths
-*   project_detect  — Detect which project a path belongs to
-*   project_health  — Audit all projects for moved/deleted directories
-*   session_route   — Auto-route session to project (path/marker/topic)
-*
-* NOTE: All tool logic lives in tools.ts (shared with the daemon).
-* This file wires MCP schema definitions to those pure functions.
-*/
-let _registryDb = null;
-let _federationDb = null;
-function getRegistryDb() {
-	if (!_registryDb) _registryDb = openRegistry();
-	return _registryDb;
-}
-function getFederationDb() {
-	if (!_federationDb) _federationDb = openFederation();
-	return _federationDb;
-}
-async function startMcpServer() {
-	const server = new McpServer({
-		name: "pai",
-		version: "0.1.0"
-	});
-	server.tool("memory_search", [
-		"Search PAI federated memory using BM25 full-text ranking, semantic similarity, or a hybrid of both.",
-		"",
-		"Use this BEFORE answering questions about past work, decisions, dates, people,",
-		"preferences, project status, todos, technical choices, or anything that might",
-		"have been recorded in session notes or memory files.",
-		"",
-		"Modes:",
-		"  keyword  — BM25 full-text search (default, fast, no embeddings required)",
-		"  semantic — Cosine similarity over vector embeddings (requires prior embed run)",
-		"  hybrid   — Normalized combination of BM25 + cosine (best quality)",
-		"",
-		"Reranking is ON by default — results are re-scored with a cross-encoder model for better relevance.",
-		"Set rerank=false to skip reranking (faster but less accurate ordering).",
-		"",
-		"Recency boost optionally down-weights older results (recency_boost=90 means scores halve every 90 days).",
-		"",
-		"Defaults come from ~/.config/pai/config.json (search section). Per-call parameters override config defaults.",
-		"",
-		"Returns ranked snippets with project slug, file path, line range, and score.",
-		"Higher score = more relevant."
-	].join("\n"), {
-		query: string().describe("Free-text search query. Multiple words are ORed together — any matching word returns a result, ranked by relevance."),
-		project: string().optional().describe("Scope search to a single project by slug. Omit to search all projects."),
-		all_projects: boolean().optional().describe("Explicitly search all projects (default behaviour when project is omitted)."),
-		sources: array(_enum(["memory", "notes"])).optional().describe("Restrict to specific source types: 'memory' or 'notes'."),
-		limit: number().int().min(1).max(100).optional().describe("Maximum results to return. Default: 10."),
-		mode: _enum([
-			"keyword",
-			"semantic",
-			"hybrid"
-		]).optional().describe("Search mode: 'keyword' (BM25, default), 'semantic' (vector cosine), or 'hybrid' (both combined)."),
-		rerank: boolean().optional().describe("Rerank results using a cross-encoder model for better relevance. Default: true. Set to false to skip reranking for faster but less accurate results."),
-		recency_boost: number().int().min(0).max(365).optional().describe("Apply recency boost: score halves every N days. 0 = off. Default from config (typically 90). Applied after reranking.")
-	}, async (args) => {
-		const config = loadConfig();
-		const result = await toolMemorySearch(getRegistryDb(), getFederationDb(), {
-			...args,
-			recencyBoost: args.recency_boost
-		}, config.search);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("memory_get", [
-		"Read the content of a specific file from a registered PAI project.",
-		"",
-		"Use this to read a full memory file, session note, or document after finding",
-		"it via memory_search. Optionally restrict to a line range.",
-		"",
-		"The path must be a relative path within the project root (no ../ traversal)."
-	].join("\n"), {
-		project: string().describe("Project slug identifying which project's files to read from."),
-		path: string().describe("Relative path within the project root (e.g. 'Notes/0001 - 2026-01-01 - Example.md')."),
-		from: number().int().min(1).optional().describe("Starting line number (1-based, inclusive). Default: 1."),
-		lines: number().int().min(1).optional().describe("Number of lines to return. Default: entire file.")
-	}, async (args) => {
-		const result = toolMemoryGet(getRegistryDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("project_info", [
-		"Get detailed information about a PAI registered project.",
-		"",
-		"Use this to look up a project's root path, type, status, tags, session count,",
-		"and last active date. If no slug is provided, attempts to detect the current",
-		"project from the caller's working directory."
-	].join("\n"), { slug: string().optional().describe("Project slug. Omit to auto-detect from the current working directory.") }, async (args) => {
-		const result = toolProjectInfo(getRegistryDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("project_list", [
-		"List registered PAI projects with optional filters.",
-		"",
-		"Use this to browse all known projects, find projects by status or tag,",
-		"or get a quick overview of the PAI registry."
-	].join("\n"), {
-		status: _enum([
-			"active",
-			"archived",
-			"migrating"
-		]).optional().describe("Filter by project status. Default: all statuses."),
-		tag: string().optional().describe("Filter by tag name (exact match)."),
-		limit: number().int().min(1).max(500).optional().describe("Maximum number of projects to return. Default: 50.")
-	}, async (args) => {
-		const result = toolProjectList(getRegistryDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("session_list", [
-		"List session notes for a PAI project.",
-		"",
-		"Use this to find what sessions exist for a project, see their dates and titles,",
-		"and identify specific session notes to read via memory_get."
-	].join("\n"), {
-		project: string().describe("Project slug to list sessions for."),
-		limit: number().int().min(1).max(500).optional().describe("Maximum sessions to return. Default: 10 (most recent first)."),
-		status: _enum([
-			"open",
-			"completed",
-			"compacted"
-		]).optional().describe("Filter by session status.")
-	}, async (args) => {
-		const result = toolSessionList(getRegistryDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("registry_search", [
-		"Search PAI project registry by slug, display name, or path.",
-		"",
-		"Use this to find the slug for a project when you know its name or path,",
-		"or to check if a project is registered. Returns matching project entries."
-	].join("\n"), { query: string().describe("Search term matched against project slugs, display names, and root paths (case-insensitive substring match).") }, async (args) => {
-		const result = toolRegistrySearch(getRegistryDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("project_detect", [
-		"Detect which registered PAI project a filesystem path belongs to.",
-		"",
-		"Use this at session start to auto-identify the current project from the",
-		"working directory, or to map any path back to its registered project.",
-		"",
-		"Returns: slug, display_name, root_path, type, status, match_type (exact|parent),",
-		"relative_path (if the given path is inside a project), and session stats.",
-		"",
-		"match_type 'exact' means the path IS the project root.",
-		"match_type 'parent' means the path is a subdirectory of the project root."
-	].join("\n"), { cwd: string().optional().describe("Absolute path to detect project for. Defaults to the MCP server's process.cwd().") }, async (args) => {
-		const result = toolProjectDetect(getRegistryDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("project_health", [
-		"Audit all registered PAI projects to find moved or deleted directories.",
-		"",
-		"Returns a JSON report categorising every project as:",
-		"  active  — root_path exists on disk",
-		"  stale   — root_path missing, but a directory with the same name was found nearby",
-		"  dead    — root_path missing, no candidate found",
-		"",
-		"Use this to diagnose orphaned sessions or missing project paths."
-	].join("\n"), { category: _enum([
-		"active",
-		"stale",
-		"dead",
-		"all"
-	]).optional().describe("Filter results to a specific health category. Default: all.") }, async (args) => {
-		const result = await toolProjectHealth(getRegistryDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("notification_config", [
-		"Query or update the PAI unified notification configuration.",
-		"",
-		"Actions:",
-		"  get  — Return the current notification mode, active channels, and routing table.",
-		"  set  — Change the notification mode or update channel/routing config.",
-		"  send — Send a notification through the configured channels.",
-		"",
-		"Notification modes:",
-		"  auto      — Use the per-event routing table (default)",
-		"  voice     — All events sent as WhatsApp voice (TTS)",
-		"  whatsapp  — All events sent as WhatsApp text",
-		"  ntfy      — All events sent to ntfy.sh",
-		"  macos     — All events sent as macOS notifications",
-		"  cli       — All events written to CLI output only",
-		"  off       — Suppress all notifications",
-		"",
-		"Event types for send: error | progress | completion | info | debug",
-		"",
-		"Examples:",
-		"  { \"action\": \"get\" }",
-		"  { \"action\": \"set\", \"mode\": \"voice\" }",
-		"  { \"action\": \"send\", \"event\": \"completion\", \"message\": \"Done!\" }"
-	].join("\n"), {
-		action: _enum([
-			"get",
-			"set",
-			"send"
-		]).describe("Action: 'get' (read config), 'set' (update config), 'send' (send notification)."),
-		mode: _enum([
-			"auto",
-			"voice",
-			"whatsapp",
-			"ntfy",
-			"macos",
-			"cli",
-			"off"
-		]).optional().describe("For action=set: new notification mode."),
-		channels: record(string(), unknown()).optional().describe("For action=set: partial channel config overrides as a JSON object. E.g. { \"whatsapp\": { \"enabled\": true }, \"macos\": { \"enabled\": false } }"),
-		routing: record(string(), unknown()).optional().describe("For action=set: partial routing overrides as a JSON object. E.g. { \"error\": [\"whatsapp\", \"macos\"], \"progress\": [\"cli\"] }"),
-		event: _enum([
-			"error",
-			"progress",
-			"completion",
-			"info",
-			"debug"
-		]).optional().describe("For action=send: event type. Default: 'info'."),
-		message: string().optional().describe("For action=send: the notification message body."),
-		title: string().optional().describe("For action=send: optional notification title (used by macOS and ntfy).")
-	}, async (args) => {
-		const result = await toolNotificationConfig(args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("topic_detect", [
-		"Detect whether recent conversation context has shifted to a different project.",
-		"",
-		"Call this when the conversation may have drifted away from the initially-routed project.",
-		"Provide a short summary of the recent context (last few messages or tool call results).",
-		"",
-		"Returns:",
-		"  shifted          — true if a topic shift was detected",
-		"  current_project  — the project the session is currently routed to",
-		"  suggested_project — the project that best matches the context",
-		"  confidence       — [0,1] fraction of memory mass held by suggested_project",
-		"  chunks_scored    — number of memory chunks that contributed to scoring",
-		"  top_matches      — top-3 projects with their confidence percentages",
-		"",
-		"A shift is reported when confidence >= threshold (default 0.6) and the",
-		"best-matching project differs from current_project.",
-		"",
-		"Use cases:",
-		"  - Call at session start to confirm routing is correct",
-		"  - Call periodically when working across multiple concerns",
-		"  - Integrate with pre-tool hooks for automatic drift detection"
-	].join("\n"), {
-		context: string().describe("Recent conversation context: a few sentences summarising what the session has been discussing. Can include file paths, feature names, commands run, or any relevant text."),
-		current_project: string().optional().describe("The project slug this session is currently routed to. If omitted, the tool still returns the best-matching project but shifted will always be false."),
-		threshold: number().min(0).max(1).optional().describe("Minimum confidence [0,1] to declare a shift. Default: 0.6. Increase to reduce false positives. Decrease to catch subtle drifts.")
-	}, async (args) => {
-		const result = await toolTopicDetect(args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("session_route", [
-		"Automatically detect which project this session belongs to.",
-		"",
-		"Call this at session start (e.g., from CLAUDE.md or a session-start hook)",
-		"to route the session to the correct project automatically.",
-		"",
-		"Detection strategy (in priority order):",
-		"  1. path   — exact or parent-directory match in the project registry",
-		"  2. marker — walk up from cwd looking for Notes/PAI.md marker files",
-		"  3. topic  — BM25 keyword search against memory (only if context provided)",
-		"",
-		"Returns:",
-		"  slug         — the matched project slug",
-		"  display_name — human-readable project name",
-		"  root_path    — absolute path to the project root",
-		"  method       — how it was detected: 'path', 'marker', or 'topic'",
-		"  confidence   — 1.0 for path/marker matches, BM25 fraction for topic",
-		"",
-		"If no match is found, returns a message explaining what was tried.",
-		"Run 'pai project add .' to register the current directory."
-	].join("\n"), {
-		cwd: string().optional().describe("Working directory to detect from. Defaults to process.cwd(). Pass the session's actual working directory for accurate detection."),
-		context: string().optional().describe("Optional conversation context for topic-based fallback routing. A few sentences summarising what the session will work on. Only used if path and marker detection both fail.")
-	}, async (args) => {
-		const result = await toolSessionRoute(getRegistryDb(), getFederationDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("zettel_explore", [
-		"Explore the vault's knowledge graph using Luhmann's Folgezettel traversal.",
-		"Follow trains of thought forward, backward, or both from a starting note.",
-		"Classifies links as sequential (same-folder) or associative (cross-folder)."
-	].join("\n"), {
-		start_note: string().describe("Path or title of the note to start traversal from."),
-		depth: number().int().min(1).max(10).optional().describe("How many link hops to traverse. Default: 3."),
-		direction: _enum([
-			"forward",
-			"backward",
-			"both"
-		]).optional().describe("Traversal direction: 'forward' (outlinks), 'backward' (backlinks), or 'both'. Default: both."),
-		mode: _enum([
-			"sequential",
-			"associative",
-			"all"
-		]).optional().describe("Link type filter: 'sequential' (same-folder), 'associative' (cross-folder), or 'all'. Default: all.")
-	}, async (args) => {
-		const result = await toolZettelExplore(getFederationDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("zettel_health", ["Audit the structural health of the Obsidian vault.", "Reports dead links, orphan notes, disconnected clusters, low-connectivity files, and an overall health score."].join("\n"), {
-		scope: _enum([
-			"full",
-			"recent",
-			"project"
-		]).optional().describe("Audit scope: 'full' (entire vault), 'recent' (recently modified), or 'project' (specific path). Default: full."),
-		project_path: string().optional().describe("Absolute path to the project/folder to audit when scope='project'."),
-		recent_days: number().int().optional().describe("Number of days to look back when scope='recent'. Default: 30."),
-		include: array(_enum([
-			"dead_links",
-			"orphans",
-			"disconnected",
-			"low_connectivity"
-		])).optional().describe("Specific checks to include. Omit to run all checks.")
-	}, async (args) => {
-		const result = await toolZettelHealth(getFederationDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("zettel_surprise", ["Find surprising connections — notes that are semantically similar to a reference note but far away in the link graph.", "High surprise = unexpected relevance."].join("\n"), {
-		reference_path: string().describe("Path to the reference note to find surprising connections for."),
-		vault_project_id: number().int().describe("Project ID of the vault to search within."),
-		limit: number().int().optional().describe("Maximum number of surprising notes to return. Default: 10."),
-		min_similarity: number().optional().describe("Minimum semantic similarity [0,1] for a note to be considered. Default: 0.5."),
-		min_graph_distance: number().int().optional().describe("Minimum link hops away from the reference note. Default: 3.")
-	}, async (args) => {
-		const result = await toolZettelSurprise(getFederationDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("zettel_suggest", ["Suggest new connections for a note using semantic similarity, shared tags, and graph neighborhood (friends-of-friends)."].join("\n"), {
-		note_path: string().describe("Path to the note to generate link suggestions for."),
-		vault_project_id: number().int().describe("Project ID of the vault to search within."),
-		limit: number().int().optional().describe("Maximum number of suggestions to return. Default: 10."),
-		exclude_linked: boolean().optional().describe("Exclude notes already linked from this note. Default: true.")
-	}, async (args) => {
-		const result = await toolZettelSuggest(getFederationDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("zettel_converse", ["Use the vault as a Zettelkasten communication partner.", "Ask a question, get relevant notes with cross-domain connections and a synthesis prompt for generating new insights."].join("\n"), {
-		question: string().describe("The question or topic to explore in the vault."),
-		vault_project_id: number().int().describe("Project ID of the vault to query."),
-		depth: number().int().optional().describe("How many link hops to follow from seed notes. Default: 2."),
-		limit: number().int().optional().describe("Maximum number of relevant notes to retrieve. Default: 10.")
-	}, async (args) => {
-		const result = await toolZettelConverse(getFederationDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	server.tool("zettel_themes", ["Detect emerging themes by clustering recent notes with similar embeddings.", "Reveals forming idea clusters and suggests index notes for unlinked clusters."].join("\n"), {
-		vault_project_id: number().int().describe("Project ID of the vault to analyse."),
-		lookback_days: number().int().optional().describe("Number of days of recent notes to cluster. Default: 30."),
-		min_cluster_size: number().int().optional().describe("Minimum notes required to form a theme cluster. Default: 3."),
-		max_themes: number().int().optional().describe("Maximum number of theme clusters to return. Default: 10."),
-		similarity_threshold: number().optional().describe("Minimum cosine similarity to group notes into a cluster [0,1]. Default: 0.7.")
-	}, async (args) => {
-		const result = await toolZettelThemes(getFederationDb(), args);
-		return {
-			content: result.content.map((c) => ({
-				type: c.type,
-				text: c.text
-			})),
-			isError: result.isError
-		};
-	});
-	const transport = new StdioServerTransport();
-	await server.connect(transport);
-}
-
-//#endregion
-//#region src/mcp/index.ts
-/**
-* PAI Knowledge OS — MCP server entry point
-*
-* When invoked as `node dist/mcp/index.mjs` (or via the `pai-mcp` bin),
-* starts the PAI MCP server on stdio transport so Claude Code can call
-* memory_search, memory_get, project_info, project_list, session_list,
-* and registry_search tools directly during conversations.
-*/
-startMcpServer().catch((err) => {
-	process.stderr.write(`PAI MCP server fatal error: ${String(err)}\n`);
-	process.exit(1);
-});
-
-//#endregion
-export {  };
-//# sourceMappingURL=index.mjs.map