@tekmidian/pai 0.9.0 → 0.9.1

package/dist/tools-8t7BQrm9.mjs.map

@@ -0,0 +1 @@
+{"version":3,"file":"tools-8t7BQrm9.mjs","names":[],"sources":["../src/mcp/tools/types.ts","../src/mcp/tools/memory.ts","../src/mcp/tools/projects.ts","../src/mcp/tools/sessions.ts","../src/mcp/tools/registry.ts","../src/mcp/tools/zettel.ts","../src/mcp/tools/kg.ts","../src/memory/wakeup.ts","../src/mcp/tools/wakeup.ts","../src/memory/taxonomy.ts","../src/mcp/tools/taxonomy.ts","../src/memory/tunnels.ts","../src/mcp/tools/tunnels.ts","../src/mcp/tools.ts"],"sourcesContent":["/**\n * Shared types and project-row helpers used across all MCP tool handler modules.\n */\n\nimport { resolve } from \"node:path\";\nimport type { Database } from \"better-sqlite3\";\n\nexport interface ToolContent {\n  type: \"text\";\n  text: string;\n}\n\nexport interface ToolResult {\n  content: ToolContent[];\n  isError?: boolean;\n}\n\n// ---------------------------------------------------------------------------\n// Shared row type — mirrors the projects SQLite schema\n// ---------------------------------------------------------------------------\n\nexport interface ProjectRow {\n  id: number;\n  slug: string;\n  display_name: string;\n  root_path: string;\n  type: string;\n  status: string;\n  created_at: number;\n  updated_at: number;\n  archived_at?: number | null;\n  parent_id?: number | null;\n  obsidian_link?: string | null;\n}\n\n// ---------------------------------------------------------------------------\n// Helper: lookup project_id by slug (also checks aliases)\n// ---------------------------------------------------------------------------\n\nexport function lookupProjectId(\n  registryDb: Database,\n  slug: string\n): number | null {\n  const bySlug = registryDb\n    .prepare(\"SELECT id FROM projects WHERE slug = ?\")\n    .get(slug) as { id: number } | undefined;\n  if (bySlug) return bySlug.id;\n\n  const byAlias = registryDb\n    .prepare(\"SELECT project_id FROM aliases WHERE alias = ?\")\n    .get(slug) as { project_id: number } | undefined;\n  if (byAlias) return byAlias.project_id;\n\n  return null;\n}\n\n// ---------------------------------------------------------------------------\n// Helper: detect project from a filesystem path\n// ---------------------------------------------------------------------------\n\nexport function detectProjectFromPath(\n  registryDb: Database,\n  fsPath: string\n): ProjectRow | null {\n  const resolved = resolve(fsPath);\n\n  const exact = registryDb\n    .prepare(\n      \"SELECT id, slug, display_name, root_path, type, status, created_at, updated_at FROM projects WHERE root_path = ?\"\n    )\n    .get(resolved) as ProjectRow | undefined;\n\n  if (exact) return exact;\n\n  const all = registryDb\n    .prepare(\n      \"SELECT id, slug, display_name, root_path, type, status, created_at, updated_at FROM projects ORDER BY LENGTH(root_path) DESC\"\n    )\n    .all() as ProjectRow[];\n\n  for (const project of all) {\n    if (\n      resolved.startsWith(project.root_path + \"/\") ||\n      resolved === project.root_path\n    ) {\n      return project;\n    }\n  }\n\n  return null;\n}\n\n// ---------------------------------------------------------------------------\n// Helper: format project row for tool output\n// ---------------------------------------------------------------------------\n\nexport function formatProject(registryDb: Database, project: ProjectRow): string {\n  const sessionCount = (\n    registryDb\n      .prepare(\"SELECT COUNT(*) AS n FROM sessions WHERE project_id = ?\")\n      .get(project.id) as { n: number }\n  ).n;\n\n  const lastSession = registryDb\n    .prepare(\n      \"SELECT date FROM sessions WHERE project_id = ? ORDER BY date DESC LIMIT 1\"\n    )\n    .get(project.id) as { date: string } | undefined;\n\n  const tags = (\n    registryDb\n      .prepare(\n        `SELECT t.name FROM tags t\n         JOIN project_tags pt ON pt.tag_id = t.id\n         WHERE pt.project_id = ?\n         ORDER BY t.name`\n      )\n      .all(project.id) as Array<{ name: string }>\n  ).map((r) => r.name);\n\n  const aliases = (\n    registryDb\n      .prepare(\"SELECT alias FROM aliases WHERE project_id = ? ORDER BY alias\")\n      .all(project.id) as Array<{ alias: string }>\n  ).map((r) => r.alias);\n\n  const lines: string[] = [\n    `slug: ${project.slug}`,\n    `display_name: ${project.display_name}`,\n    `root_path: ${project.root_path}`,\n    `type: ${project.type}`,\n    `status: ${project.status}`,\n    `sessions: ${sessionCount}`,\n  ];\n\n  if (lastSession) lines.push(`last_session: ${lastSession.date}`);\n  if (tags.length) lines.push(`tags: ${tags.join(\", \")}`);\n  if (aliases.length) lines.push(`aliases: ${aliases.join(\", \")}`);\n  if (project.obsidian_link) lines.push(`obsidian_link: ${project.obsidian_link}`);\n  if (project.archived_at) {\n    lines.push(\n      `archived_at: ${new Date(project.archived_at).toISOString().slice(0, 10)}`\n    );\n  }\n\n  return lines.join(\"\\n\");\n}\n","/**\n * MCP tool handlers: memory_search, memory_get\n */\n\nimport { readFileSync, existsSync, statSync } from \"node:fs\";\nimport { join, resolve, isAbsolute } from \"node:path\";\nimport type { Database } from \"better-sqlite3\";\nimport { populateSlugs, searchMemoryHybrid } from \"../../memory/search.js\";\nimport type { StorageBackend } from \"../../storage/interface.js\";\nimport type { SearchConfig } from \"../../daemon/config.js\";\nimport type { SearchResult } from \"../../memory/search.js\";\nimport {\n  lookupProjectId,\n  type ToolResult,\n} from \"./types.js\";\n\n// ---------------------------------------------------------------------------\n// Tool: memory_search\n// ---------------------------------------------------------------------------\n\nexport interface MemorySearchParams {\n  query: string;\n  project?: string;\n  all_projects?: boolean;\n  sources?: Array<\"memory\" | \"notes\">;\n  limit?: number;\n  mode?: \"keyword\" | \"semantic\" | \"hybrid\";\n  /** Rerank results using cross-encoder model for better relevance ordering. */\n  rerank?: boolean;\n  /** Apply recency boost — score decays by half every N days. 0 = off (default). */\n  recencyBoost?: number;\n  /** Maximum characters per result snippet. Default 200.\n   *  Limit context consumption — MCP results go into Claude's context window. */\n  snippetLength?: number;\n}\n\nexport async function toolMemorySearch(\n  registryDb: Database,\n  federation: Database | StorageBackend,\n  params: MemorySearchParams,\n  searchDefaults?: SearchConfig,\n): Promise<ToolResult> {\n  try {\n    const projectIds: number[] | undefined = params.project\n      ? (() => {\n          const id = lookupProjectId(registryDb, params.project!);\n          return id != null ? [id] : [];\n        })()\n      : undefined;\n\n    if (params.project && (!projectIds || projectIds.length === 0)) {\n      return {\n        content: [\n          { type: \"text\", text: `Project not found: ${params.project}` },\n        ],\n        isError: true,\n      };\n    }\n\n    // NOTE: No indexAll() here — indexing is handled by the daemon scheduler.\n    // The daemon ensures the index stays fresh; the search hot path is read-only.\n\n    const mode = params.mode ?? (searchDefaults?.mode ?? \"keyword\");\n    // Limit context consumption — MCP results go into Claude's context window.\n    // Default to 5 results and 200-char snippets to keep a single search call\n    // within ~1-2K tokens rather than 5K+.\n    const snippetLength = params.snippetLength ?? (searchDefaults?.snippetLength ?? 200);\n    const searchOpts = {\n      projectIds,\n      sources: params.sources,\n      maxResults: params.limit ?? (searchDefaults?.defaultLimit ?? 5),\n    };\n\n    let results;\n\n    // Determine if federation is a StorageBackend or a raw Database\n    const isBackend = (x: Database | StorageBackend): x is StorageBackend =>\n      \"backendType\" in x;\n\n    if (isBackend(federation)) {\n      // Use the storage backend interface (works for both SQLite and Postgres)\n      if (mode === \"keyword\") {\n        results = await federation.searchKeyword(params.query, searchOpts);\n      } else if (mode === \"semantic\" || mode === \"hybrid\") {\n        const { generateEmbedding } = await import(\"../../memory/embeddings.js\");\n        const queryEmbedding = await generateEmbedding(params.query, true);\n\n        if (mode === \"semantic\") {\n          results = await federation.searchSemantic(queryEmbedding, searchOpts);\n        } else {\n          // Hybrid: combine keyword + semantic\n          const [kwResults, semResults] = await Promise.all([\n            federation.searchKeyword(params.query, { ...searchOpts, maxResults: 50 }),\n            federation.searchSemantic(queryEmbedding, { ...searchOpts, maxResults: 50 }),\n          ]); // 50 candidates is sufficient for min-max normalization\n          // Reuse the existing hybrid scoring logic\n          results = combineHybridResults(kwResults, semResults, searchOpts.maxResults ?? 10);\n        }\n      } else {\n        results = await federation.searchKeyword(params.query, searchOpts);\n      }\n    } else {\n      // Legacy path: raw better-sqlite3 Database (for direct MCP server usage)\n      const { searchMemory, searchMemorySemantic } = await import(\"../../memory/search.js\");\n\n      if (mode === \"keyword\") {\n        results = searchMemory(federation, params.query, searchOpts);\n      } else if (mode === \"semantic\" || mode === \"hybrid\") {\n        const { generateEmbedding } = await import(\"../../memory/embeddings.js\");\n        const queryEmbedding = await generateEmbedding(params.query, true);\n\n        if (mode === \"semantic\") {\n          results = searchMemorySemantic(federation, queryEmbedding, searchOpts);\n        } else {\n          results = searchMemoryHybrid(\n            federation,\n            params.query,\n            queryEmbedding,\n            searchOpts\n          );\n        }\n      } else {\n        results = searchMemory(federation, params.query, searchOpts);\n      }\n    }\n\n    // Cross-encoder reranking (on by default)\n    const shouldRerank = params.rerank ?? (searchDefaults?.rerank ?? true);\n    if (shouldRerank && results.length > 0) {\n      const { rerankResults } = await import(\"../../memory/reranker.js\");\n      results = await rerankResults(params.query, results, {\n        topK: searchOpts.maxResults ?? 5,\n      });\n    }\n\n    // Recency boost (off by default, applied after reranking)\n    const recencyDays = params.recencyBoost ?? (searchDefaults?.recencyBoostDays ?? 0);\n    if (recencyDays > 0 && results.length > 0) {\n      const { applyRecencyBoost } = await import(\"../../memory/search.js\");\n      results = applyRecencyBoost(results, recencyDays);\n    }\n\n    const withSlugs = populateSlugs(results, registryDb);\n\n    if (withSlugs.length === 0) {\n      return {\n        content: [\n          {\n            type: \"text\",\n            text: `No results found for query: \"${params.query}\" (mode: ${mode})`,\n          },\n        ],\n      };\n    }\n\n    const rerankLabel = shouldRerank ? \" +rerank\" : \"\";\n    const formatted = withSlugs\n      .map((r, i) => {\n        const header = `[${i + 1}] ${r.projectSlug ?? `project:${r.projectId}`} — ${r.path} (lines ${r.startLine}-${r.endLine}) score=${r.score.toFixed(4)} tier=${r.tier} source=${r.source}`;\n        // Truncate snippet to snippetLength — limit context consumption.\n        // MCP results go into Claude's context window; keep each result tight.\n        const raw = r.snippet.trim();\n        const snippet = raw.length > snippetLength\n          ? raw.slice(0, snippetLength) + \"...\"\n          : raw;\n        return `${header}\\n${snippet}`;\n      })\n      .join(\"\\n\\n---\\n\\n\");\n\n    // Query feedback loop: save query + result metadata for future indexing\n    try {\n      const { saveQueryResult } = await import(\"../../zettelkasten/query-feedback.js\");\n      saveQueryResult({\n        query: params.query,\n        timestamp: Date.now(),\n        source: \"memory_search\",\n        sourceSlugs: withSlugs.slice(0, 5).map((r) => r.path),\n        answerPreview: withSlugs.slice(0, 3).map((r) => r.snippet.trim().slice(0, 150)).join(\" | \"),\n        resultCount: withSlugs.length,\n      });\n    } catch {\n      // Non-critical — don't fail the search if feedback logging errors\n    }\n\n    return {\n      content: [\n        {\n          type: \"text\",\n          text: `Found ${withSlugs.length} result(s) for \"${params.query}\" (mode: ${mode}${rerankLabel}):\\n\\n${formatted}`,\n        },\n      ],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `Search error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: memory_get\n// ---------------------------------------------------------------------------\n\nexport interface MemoryGetParams {\n  project: string;\n  path: string;\n  from?: number;\n  lines?: number;\n}\n\nexport function toolMemoryGet(\n  registryDb: Database,\n  params: MemoryGetParams\n): ToolResult {\n  try {\n    const projectId = lookupProjectId(registryDb, params.project);\n    if (projectId == null) {\n      return {\n        content: [\n          { type: \"text\", text: `Project not found: ${params.project}` },\n        ],\n        isError: true,\n      };\n    }\n\n    const project = registryDb\n      .prepare(\"SELECT root_path FROM projects WHERE id = ?\")\n      .get(projectId) as { root_path: string } | undefined;\n\n    if (!project) {\n      return {\n        content: [\n          { type: \"text\", text: `Project not found: ${params.project}` },\n        ],\n        isError: true,\n      };\n    }\n\n    const requestedPath = params.path;\n    if (requestedPath.includes(\"..\") || isAbsolute(requestedPath)) {\n      return {\n        content: [\n          {\n            type: \"text\",\n            text: `Invalid path: ${params.path} (must be a relative path within the project root, no ../ allowed)`,\n          },\n        ],\n        isError: true,\n      };\n    }\n\n    const fullPath = join(project.root_path, requestedPath);\n    const resolvedFull = resolve(fullPath);\n    const resolvedRoot = resolve(project.root_path);\n\n    if (\n      !resolvedFull.startsWith(resolvedRoot + \"/\") &&\n      resolvedFull !== resolvedRoot\n    ) {\n      return {\n        content: [\n          { type: \"text\", text: `Path traversal blocked: ${params.path}` },\n        ],\n        isError: true,\n      };\n    }\n\n    if (!existsSync(fullPath)) {\n      return {\n        content: [\n          {\n            type: \"text\",\n            text: `File not found: ${requestedPath} (project: ${params.project})`,\n          },\n        ],\n        isError: true,\n      };\n    }\n\n    const stat = statSync(fullPath);\n    if (stat.size > 5 * 1024 * 1024) {\n      return {\n        content: [\n          {\n            type: \"text\",\n            text: `Error: file too large (${(stat.size / 1024 / 1024).toFixed(1)} MB). Maximum 5 MB.`,\n          },\n        ],\n      };\n    }\n\n    const content = readFileSync(fullPath, \"utf8\");\n    const allLines = content.split(\"\\n\");\n\n    const fromLine = (params.from ?? 1) - 1;\n    const toLine =\n      params.lines != null\n        ? Math.min(fromLine + params.lines, allLines.length)\n        : allLines.length;\n\n    const selectedLines = allLines.slice(fromLine, toLine);\n    const text = selectedLines.join(\"\\n\");\n\n    const header =\n      params.from != null\n        ? `${params.project}/${requestedPath} (lines ${fromLine + 1}-${toLine}):`\n        : `${params.project}/${requestedPath}:`;\n\n    return {\n      content: [{ type: \"text\", text: `${header}\\n\\n${text}` }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `Read error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Hybrid search helper (backend-agnostic)\n// ---------------------------------------------------------------------------\n\n/**\n * Combine keyword + semantic results using min-max normalized scoring.\n * Mirrors the logic in searchMemoryHybrid() from memory/search.ts,\n * but works on pre-computed result arrays so it works for any backend.\n */\nexport function combineHybridResults(\n  keywordResults: SearchResult[],\n  semanticResults: SearchResult[],\n  maxResults: number,\n  keywordWeight = 0.5,\n  semanticWeight = 0.5\n): SearchResult[] {\n  if (keywordResults.length === 0 && semanticResults.length === 0) return [];\n\n  const keyFor = (r: SearchResult) =>\n    `${r.projectId}:${r.path}:${r.startLine}:${r.endLine}`;\n\n  function minMaxNormalize(items: SearchResult[]): Map<string, number> {\n    if (items.length === 0) return new Map();\n    const min = Math.min(...items.map((r) => r.score));\n    const max = Math.max(...items.map((r) => r.score));\n    const range = max - min;\n    const m = new Map<string, number>();\n    for (const r of items) {\n      m.set(keyFor(r), range === 0 ? 1 : (r.score - min) / range);\n    }\n    return m;\n  }\n\n  const kwNorm = minMaxNormalize(keywordResults);\n  const semNorm = minMaxNormalize(semanticResults);\n\n  const allKeys = new Set<string>([\n    ...keywordResults.map(keyFor),\n    ...semanticResults.map(keyFor),\n  ]);\n\n  const metaMap = new Map<string, SearchResult>();\n  for (const r of [...keywordResults, ...semanticResults]) {\n    metaMap.set(keyFor(r), r);\n  }\n\n  const combined: Array<SearchResult & { combinedScore: number }> = [];\n  for (const key of allKeys) {\n    const meta = metaMap.get(key)!;\n    const kwScore = kwNorm.get(key) ?? 0;\n    const semScore = semNorm.get(key) ?? 0;\n    const combinedScore = keywordWeight * kwScore + semanticWeight * semScore;\n    combined.push({ ...meta, score: combinedScore, combinedScore });\n  }\n\n  return combined\n    .sort((a, b) => b.score - a.score)\n    .slice(0, maxResults)\n    .map(({ combinedScore: _unused, ...r }) => r);\n}\n","/**\n * MCP tool handlers: project_info, project_list, project_detect,\n *                    project_health, project_todo\n */\n\nimport { readFileSync, existsSync } from \"node:fs\";\nimport { join } from \"node:path\";\nimport type { Database } from \"better-sqlite3\";\nimport { detectProject, formatDetectionJson } from \"../../cli/commands/detect.js\";\nimport {\n  lookupProjectId,\n  detectProjectFromPath,\n  formatProject,\n  type ProjectRow,\n  type ToolResult,\n} from \"./types.js\";\n\n// ---------------------------------------------------------------------------\n// Tool: project_info\n// ---------------------------------------------------------------------------\n\nexport interface ProjectInfoParams {\n  slug?: string;\n}\n\nexport function toolProjectInfo(\n  registryDb: Database,\n  params: ProjectInfoParams\n): ToolResult {\n  try {\n    let project: ProjectRow | null = null;\n\n    if (params.slug) {\n      const projectId = lookupProjectId(registryDb, params.slug);\n      if (projectId != null) {\n        project = registryDb\n          .prepare(\n            \"SELECT id, slug, display_name, root_path, type, status, created_at, updated_at, archived_at, parent_id, obsidian_link FROM projects WHERE id = ?\"\n          )\n          .get(projectId) as ProjectRow | null;\n      }\n    } else {\n      const cwd = process.cwd();\n      project = detectProjectFromPath(registryDb, cwd);\n    }\n\n    if (!project) {\n      const message = params.slug\n        ? `Project not found: ${params.slug}`\n        : `No PAI project found matching the current directory: ${process.cwd()}`;\n      return {\n        content: [{ type: \"text\", text: message }],\n        isError: !params.slug,\n      };\n    }\n\n    return {\n      content: [{ type: \"text\", text: formatProject(registryDb, project) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `project_info error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: project_list\n// ---------------------------------------------------------------------------\n\nexport interface ProjectListParams {\n  status?: \"active\" | \"archived\" | \"migrating\";\n  tag?: string;\n  limit?: number;\n}\n\nexport function toolProjectList(\n  registryDb: Database,\n  params: ProjectListParams\n): ToolResult {\n  try {\n    const conditions: string[] = [];\n    const queryParams: (string | number)[] = [];\n\n    if (params.status) {\n      conditions.push(\"p.status = ?\");\n      queryParams.push(params.status);\n    }\n\n    if (params.tag) {\n      conditions.push(\n        \"p.id IN (SELECT pt.project_id FROM project_tags pt JOIN tags t ON pt.tag_id = t.id WHERE t.name = ?)\"\n      );\n      queryParams.push(params.tag);\n    }\n\n    const where =\n      conditions.length > 0 ? `WHERE ${conditions.join(\" AND \")}` : \"\";\n    const limit = params.limit ?? 50;\n    queryParams.push(limit);\n\n    const projects = registryDb\n      .prepare(\n        `SELECT p.id, p.slug, p.display_name, p.root_path, p.type, p.status, p.updated_at\n         FROM projects p\n         ${where}\n         ORDER BY p.updated_at DESC\n         LIMIT ?`\n      )\n      .all(...queryParams) as Array<{\n      id: number;\n      slug: string;\n      display_name: string;\n      root_path: string;\n      type: string;\n      status: string;\n      updated_at: number;\n    }>;\n\n    if (projects.length === 0) {\n      return {\n        content: [\n          {\n            type: \"text\",\n            text: \"No projects found matching the given filters.\",\n          },\n        ],\n      };\n    }\n\n    const lines = projects.map(\n      (p) =>\n        `${p.slug}  [${p.status}]  ${p.root_path}  (updated: ${new Date(p.updated_at).toISOString().slice(0, 10)})`\n    );\n\n    return {\n      content: [\n        {\n          type: \"text\",\n          text: `${projects.length} project(s):\\n\\n${lines.join(\"\\n\")}`,\n        },\n      ],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `project_list error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: project_detect\n// ---------------------------------------------------------------------------\n\nexport interface ProjectDetectParams {\n  cwd?: string;\n}\n\nexport function toolProjectDetect(\n  registryDb: Database,\n  params: ProjectDetectParams\n): ToolResult {\n  try {\n    const detection = detectProject(registryDb, params.cwd);\n\n    if (!detection) {\n      const target = params.cwd ?? process.cwd();\n      return {\n        content: [\n          {\n            type: \"text\",\n            text: `No registered project found for path: ${target}\\n\\nRun 'pai project add .' to register this directory.`,\n          },\n        ],\n      };\n    }\n\n    return {\n      content: [{ type: \"text\", text: formatDetectionJson(detection) }],\n    };\n  } catch (e) {\n    return {\n      content: [\n        { type: \"text\", text: `project_detect error: ${String(e)}` },\n      ],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: project_health\n// ---------------------------------------------------------------------------\n\nexport interface ProjectHealthParams {\n  category?: \"active\" | \"stale\" | \"dead\" | \"all\";\n}\n\nexport async function toolProjectHealth(\n  registryDb: Database,\n  params: ProjectHealthParams\n): Promise<ToolResult> {\n  try {\n    const { existsSync: fsExists, readdirSync, statSync } = await import(\n      \"node:fs\"\n    );\n    const {\n      join: pathJoin,\n      basename: pathBasename,\n    } = await import(\"node:path\");\n    const { homedir } = await import(\"node:os\");\n    const { encodeDir: enc } = await import(\"../../cli/utils.js\");\n\n    interface HealthRowLocal {\n      id: number;\n      slug: string;\n      display_name: string;\n      root_path: string;\n      encoded_dir: string;\n      status: string;\n      type: string;\n      session_count: number;\n    }\n\n    const rows = registryDb\n      .prepare(\n        `SELECT p.id, p.slug, p.display_name, p.root_path, p.encoded_dir, p.status, p.type,\n           (SELECT COUNT(*) FROM sessions s WHERE s.project_id = p.id) AS session_count\n         FROM projects p\n         ORDER BY p.slug ASC`\n      )\n      .all() as HealthRowLocal[];\n\n    const home = homedir();\n    const claudeProjects = pathJoin(home, \".claude\", \"projects\");\n\n    function suggestMoved(rootPath: string): string | undefined {\n      const name = pathBasename(rootPath);\n      const candidates = [\n        pathJoin(home, \"dev\", name),\n        pathJoin(home, \"dev\", \"ai\", name),\n        pathJoin(home, \"Desktop\", name),\n        pathJoin(home, \"Projects\", name),\n      ];\n      return candidates.find((c) => fsExists(c));\n    }\n\n    function hasClaudeNotes(encodedDir: string): boolean {\n      if (!fsExists(claudeProjects)) return false;\n      try {\n        for (const entry of readdirSync(claudeProjects)) {\n          if (entry !== encodedDir && !entry.startsWith(encodedDir)) continue;\n          const full = pathJoin(claudeProjects, entry);\n          try {\n            if (!statSync(full).isDirectory()) continue;\n          } catch {\n            continue;\n          }\n          if (fsExists(pathJoin(full, \"Notes\"))) return true;\n        }\n      } catch {\n        /* ignore */\n      }\n      return false;\n    }\n\n    interface HealthResult {\n      slug: string;\n      display_name: string;\n      root_path: string;\n      status: string;\n      type: string;\n      session_count: number;\n      health: string;\n      suggested_path: string | null;\n      has_claude_notes: boolean;\n      todo: {\n        found: boolean;\n        path: string | null;\n        has_continue: boolean;\n      };\n    }\n\n    function findTodoForProject(rootPath: string): {\n      found: boolean;\n      path: string | null;\n      has_continue: boolean;\n    } {\n      const locs = [\n        \"Notes/TODO.md\",\n        \".claude/Notes/TODO.md\",\n        \"tasks/todo.md\",\n        \"TODO.md\",\n      ];\n      for (const rel of locs) {\n        const full = pathJoin(rootPath, rel);\n        if (fsExists(full)) {\n          try {\n            const raw = readFileSync(full, \"utf8\");\n            const hasContinue = /^## Continue$/m.test(raw);\n            return { found: true, path: rel, has_continue: hasContinue };\n          } catch {\n            return { found: true, path: rel, has_continue: false };\n          }\n        }\n      }\n      return { found: false, path: null, has_continue: false };\n    }\n\n    const results: HealthResult[] = rows.map((p) => {\n      const pathExists = fsExists(p.root_path);\n      let health: string;\n      let suggestedPath: string | null = null;\n\n      if (pathExists) {\n        health = \"active\";\n      } else {\n        suggestedPath = suggestMoved(p.root_path) ?? null;\n        health = suggestedPath ? \"stale\" : \"dead\";\n      }\n\n      const todo = pathExists\n        ? findTodoForProject(p.root_path)\n        : { found: false, path: null, has_continue: false };\n\n      return {\n        slug: p.slug,\n        display_name: p.display_name,\n        root_path: p.root_path,\n        status: p.status,\n        type: p.type,\n        session_count: p.session_count,\n        health,\n        suggested_path: suggestedPath,\n        has_claude_notes: hasClaudeNotes(p.encoded_dir),\n        todo,\n      };\n    });\n\n    const filtered =\n      !params.category || params.category === \"all\"\n        ? results\n        : results.filter((r) => r.health === params.category);\n\n    const summary = {\n      total: rows.length,\n      active: results.filter((r) => r.health === \"active\").length,\n      stale: results.filter((r) => r.health === \"stale\").length,\n      dead: results.filter((r) => r.health === \"dead\").length,\n    };\n\n    return {\n      content: [\n        {\n          type: \"text\",\n          text: JSON.stringify({ summary, projects: filtered }, null, 2),\n        },\n      ],\n    };\n  } catch (e) {\n    return {\n      content: [\n        { type: \"text\", text: `project_health error: ${String(e)}` },\n      ],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: project_todo\n// ---------------------------------------------------------------------------\n\nexport interface ProjectTodoParams {\n  project?: string;\n}\n\n/**\n * TODO candidate locations searched in priority order.\n * Returns the first one that exists, along with its label.\n */\nconst TODO_LOCATIONS = [\n  { rel: \"Notes/TODO.md\",       label: \"Notes/TODO.md\" },\n  { rel: \".claude/Notes/TODO.md\", label: \".claude/Notes/TODO.md\" },\n  { rel: \"tasks/todo.md\",       label: \"tasks/todo.md\" },\n  { rel: \"TODO.md\",             label: \"TODO.md\" },\n];\n\n/**\n * Given TODO file content, extract and surface the ## Continue section first,\n * then return the remaining content. Returns an object with:\n *   continueSection: string | null\n *   fullContent: string\n *   hasContinue: boolean\n */\nfunction parseTodoContent(raw: string): {\n  continueSection: string | null;\n  fullContent: string;\n  hasContinue: boolean;\n} {\n  const lines = raw.split(\"\\n\");\n\n  // Find the ## Continue heading\n  const continueIdx = lines.findIndex(\n    (l) => l.trim() === \"## Continue\"\n  );\n\n  if (continueIdx === -1) {\n    return { continueSection: null, fullContent: raw, hasContinue: false };\n  }\n\n  // The section ends at the first `---` separator or next `##` heading after\n  // the Continue heading (whichever comes first).\n  let endIdx = lines.length;\n  for (let i = continueIdx + 1; i < lines.length; i++) {\n    const trimmed = lines[i].trim();\n    if (trimmed === \"---\" || (trimmed.startsWith(\"##\") && trimmed !== \"## Continue\")) {\n      endIdx = i;\n      break;\n    }\n  }\n\n  const continueLines = lines.slice(continueIdx, endIdx);\n  const continueSection = continueLines.join(\"\\n\").trim();\n\n  return { continueSection, fullContent: raw, hasContinue: true };\n}\n\nexport function toolProjectTodo(\n  registryDb: Database,\n  params: ProjectTodoParams\n): ToolResult {\n  try {\n    let rootPath: string;\n    let projectSlug: string;\n\n    if (params.project) {\n      const projectId = lookupProjectId(registryDb, params.project);\n      if (projectId == null) {\n        return {\n          content: [\n            { type: \"text\", text: `Project not found: ${params.project}` },\n          ],\n          isError: true,\n        };\n      }\n\n      const row = registryDb\n        .prepare(\"SELECT root_path, slug FROM projects WHERE id = ?\")\n        .get(projectId) as { root_path: string; slug: string } | undefined;\n\n      if (!row) {\n        return {\n          content: [\n            { type: \"text\", text: `Project not found: ${params.project}` },\n          ],\n          isError: true,\n        };\n      }\n\n      rootPath = row.root_path;\n      projectSlug = row.slug;\n    } else {\n      // Auto-detect from cwd\n      const project = detectProjectFromPath(registryDb, process.cwd());\n      if (!project) {\n        return {\n          content: [\n            {\n              type: \"text\",\n              text: `No PAI project found matching the current directory: ${process.cwd()}\\n\\nProvide a project slug or run 'pai project add .' to register this directory.`,\n            },\n          ],\n        };\n      }\n      rootPath = project.root_path;\n      projectSlug = project.slug;\n    }\n\n    // Search for TODO in priority order\n    for (const loc of TODO_LOCATIONS) {\n      const fullPath = join(rootPath, loc.rel);\n      if (existsSync(fullPath)) {\n        const raw = readFileSync(fullPath, \"utf8\");\n        const { continueSection, fullContent, hasContinue } = parseTodoContent(raw);\n\n        let output: string;\n        if (hasContinue && continueSection) {\n          // Surface the ## Continue section first, then the full content\n          output = [\n            `TODO found: ${projectSlug}/${loc.label}`,\n            \"\",\n            \"=== CONTINUE SECTION (surfaced first) ===\",\n            continueSection,\n            \"\",\n            \"=== FULL TODO CONTENT ===\",\n            fullContent,\n          ].join(\"\\n\");\n        } else {\n          output = [\n            `TODO found: ${projectSlug}/${loc.label}`,\n            \"\",\n            fullContent,\n          ].join(\"\\n\");\n        }\n\n        return {\n          content: [{ type: \"text\", text: output }],\n        };\n      }\n    }\n\n    // No TODO found in any location\n    const searched = TODO_LOCATIONS.map((l) => `  ${rootPath}/${l.rel}`).join(\"\\n\");\n    return {\n      content: [\n        {\n          type: \"text\",\n          text: [\n            `No TODO.md found for project: ${projectSlug}`,\n            \"\",\n            \"Searched locations (in order):\",\n            searched,\n            \"\",\n            \"Create a TODO with: echo '## Tasks\\\\n- [ ] First task' > Notes/TODO.md\",\n          ].join(\"\\n\"),\n        },\n      ],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `project_todo error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n","/**\n * MCP tool handlers: session_list, session_route\n */\n\nimport type { Database } from \"better-sqlite3\";\nimport type { StorageBackend } from \"../../storage/interface.js\";\nimport {\n  lookupProjectId,\n  type ToolResult,\n} from \"./types.js\";\n\n// ---------------------------------------------------------------------------\n// Tool: session_list\n// ---------------------------------------------------------------------------\n\nexport interface SessionListParams {\n  project: string;\n  limit?: number;\n  status?: \"open\" | \"completed\" | \"compacted\";\n}\n\nexport function toolSessionList(\n  registryDb: Database,\n  params: SessionListParams\n): ToolResult {\n  try {\n    const projectId = lookupProjectId(registryDb, params.project);\n    if (projectId == null) {\n      return {\n        content: [\n          { type: \"text\", text: `Project not found: ${params.project}` },\n        ],\n        isError: true,\n      };\n    }\n\n    const conditions = [\"project_id = ?\"];\n    const queryParams: (string | number)[] = [projectId];\n\n    if (params.status) {\n      conditions.push(\"status = ?\");\n      queryParams.push(params.status);\n    }\n\n    const limit = params.limit ?? 10;\n    queryParams.push(limit);\n\n    const sessions = registryDb\n      .prepare(\n        `SELECT number, date, title, filename, status\n         FROM sessions\n         WHERE ${conditions.join(\" AND \")}\n         ORDER BY number DESC\n         LIMIT ?`\n      )\n      .all(...queryParams) as Array<{\n      number: number;\n      date: string;\n      title: string;\n      filename: string;\n      status: string;\n    }>;\n\n    if (sessions.length === 0) {\n      return {\n        content: [\n          {\n            type: \"text\",\n            text: `No sessions found for project: ${params.project}`,\n          },\n        ],\n      };\n    }\n\n    const lines = sessions.map(\n      (s) =>\n        `#${String(s.number).padStart(4, \"0\")}  ${s.date}  [${s.status}]  ${s.title}\\n        file: Notes/${s.filename}`\n    );\n\n    return {\n      content: [\n        {\n          type: \"text\",\n          text: `${sessions.length} session(s) for ${params.project}:\\n\\n${lines.join(\"\\n\\n\")}`,\n        },\n      ],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `session_list error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: session_route\n// ---------------------------------------------------------------------------\n\nexport interface SessionRouteParams {\n  /** Working directory to route from (defaults to process.cwd()) */\n  cwd?: string;\n  /** Optional conversation context for topic-based fallback routing */\n  context?: string;\n}\n\n/**\n * Automatically suggest which project a session belongs to.\n *\n * Strategy (in priority order):\n *   1. path   — exact or parent-directory match in the project registry\n *   2. marker — walk up from cwd looking for Notes/PAI.md\n *   3. topic  — BM25 keyword search against memory (requires context)\n *\n * Call this at session start (e.g., from CLAUDE.md or a session-start hook)\n * to automatically route the session to the correct project.\n */\nexport async function toolSessionRoute(\n  registryDb: Database,\n  federation: Database | StorageBackend,\n  params: SessionRouteParams\n): Promise<ToolResult> {\n  try {\n    const { autoRoute, formatAutoRouteJson } = await import(\"../../session/auto-route.js\");\n\n    const result = await autoRoute(\n      registryDb,\n      federation,\n      params.cwd,\n      params.context\n    );\n\n    if (!result) {\n      const target = params.cwd ?? process.cwd();\n      return {\n        content: [\n          {\n            type: \"text\",\n            text: [\n              `No project match found for: ${target}`,\n              \"\",\n              \"Tried: path match, PAI.md marker walk\" +\n                (params.context ? \", topic detection\" : \"\"),\n              \"\",\n              \"Run 'pai project add .' to register this directory,\",\n              \"or provide conversation context for topic-based routing.\",\n            ].join(\"\\n\"),\n          },\n        ],\n      };\n    }\n\n    return {\n      content: [{ type: \"text\", text: formatAutoRouteJson(result) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `session_route error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n","/**\n * MCP tool handler: registry_search\n */\n\nimport type { Database } from \"better-sqlite3\";\nimport type { ToolResult } from \"./types.js\";\n\n// ---------------------------------------------------------------------------\n// Tool: registry_search\n// ---------------------------------------------------------------------------\n\nexport interface RegistrySearchParams {\n  query: string;\n}\n\nexport function toolRegistrySearch(\n  registryDb: Database,\n  params: RegistrySearchParams\n): ToolResult {\n  try {\n    const q = `%${params.query}%`;\n    const projects = registryDb\n      .prepare(\n        `SELECT id, slug, display_name, root_path, type, status, updated_at\n         FROM projects\n         WHERE slug LIKE ?\n            OR display_name LIKE ?\n            OR root_path LIKE ?\n         ORDER BY updated_at DESC\n         LIMIT 20`\n      )\n      .all(q, q, q) as Array<{\n      id: number;\n      slug: string;\n      display_name: string;\n      root_path: string;\n      type: string;\n      status: string;\n      updated_at: number;\n    }>;\n\n    if (projects.length === 0) {\n      return {\n        content: [\n          {\n            type: \"text\",\n            text: `No projects found matching: \"${params.query}\"`,\n          },\n        ],\n      };\n    }\n\n    const lines = projects.map((p) => `${p.slug}  [${p.status}]  ${p.root_path}`);\n\n    return {\n      content: [\n        {\n          type: \"text\",\n          text: `${projects.length} match(es) for \"${params.query}\":\\n\\n${lines.join(\"\\n\")}`,\n        },\n      ],\n    };\n  } catch (e) {\n    return {\n      content: [\n        { type: \"text\", text: `registry_search error: ${String(e)}` },\n      ],\n      isError: true,\n    };\n  }\n}\n","/**\n * MCP tool handlers: zettel_explore, zettel_health, zettel_surprise,\n *                    zettel_suggest, zettel_converse, zettel_themes,\n *                    zettel_god_notes, zettel_communities\n */\n\nimport type { StorageBackend } from \"../../storage/interface.js\";\nimport type { ToolResult } from \"./types.js\";\n\n// ---------------------------------------------------------------------------\n// Tool: zettel_explore\n// ---------------------------------------------------------------------------\n\nexport interface ZettelExploreParams {\n  start_note: string;\n  depth?: number;\n  direction?: string;\n  mode?: string;\n}\n\nexport async function toolZettelExplore(\n  backend: StorageBackend,\n  params: ZettelExploreParams\n): Promise<ToolResult> {\n  try {\n    const { zettelExplore } = await import(\"../../zettelkasten/index.js\");\n    const result = await zettelExplore(backend, {\n      startNote: params.start_note,\n      depth: params.depth,\n      direction: params.direction as \"forward\" | \"backward\" | \"both\" | undefined,\n      mode: params.mode as \"sequential\" | \"associative\" | \"all\" | undefined,\n    });\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(result, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `zettel_explore error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: zettel_health\n// ---------------------------------------------------------------------------\n\nexport interface ZettelHealthParams {\n  scope?: string;\n  project_path?: string;\n  recent_days?: number;\n  include?: string[];\n}\n\nexport async function toolZettelHealth(\n  backend: StorageBackend,\n  params: ZettelHealthParams\n): Promise<ToolResult> {\n  try {\n    const { zettelHealth } = await import(\"../../zettelkasten/index.js\");\n    const result = await zettelHealth(backend, {\n      scope: params.scope as \"full\" | \"recent\" | \"project\" | undefined,\n      projectPath: params.project_path,\n      recentDays: params.recent_days,\n      include: params.include as Array<\"dead_links\" | \"orphans\" | \"disconnected\" | \"low_connectivity\"> | undefined,\n    });\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(result, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `zettel_health error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: zettel_surprise\n// ---------------------------------------------------------------------------\n\nexport interface ZettelSurpriseParams {\n  reference_path: string;\n  vault_project_id: number;\n  limit?: number;\n  min_similarity?: number;\n  min_graph_distance?: number;\n}\n\nexport async function toolZettelSurprise(\n  backend: StorageBackend,\n  params: ZettelSurpriseParams\n): Promise<ToolResult> {\n  try {\n    const { zettelSurprise } = await import(\"../../zettelkasten/index.js\");\n    const results = await zettelSurprise(backend, {\n      referencePath: params.reference_path,\n      vaultProjectId: params.vault_project_id,\n      limit: params.limit,\n      minSimilarity: params.min_similarity,\n      minGraphDistance: params.min_graph_distance,\n    });\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(results, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `zettel_surprise error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: zettel_suggest\n// ---------------------------------------------------------------------------\n\nexport interface ZettelSuggestParams {\n  note_path: string;\n  vault_project_id: number;\n  limit?: number;\n  exclude_linked?: boolean;\n}\n\nexport async function toolZettelSuggest(\n  backend: StorageBackend,\n  params: ZettelSuggestParams\n): Promise<ToolResult> {\n  try {\n    const { zettelSuggest } = await import(\"../../zettelkasten/index.js\");\n    const results = await zettelSuggest(backend, {\n      notePath: params.note_path,\n      vaultProjectId: params.vault_project_id,\n      limit: params.limit,\n      excludeLinked: params.exclude_linked,\n    });\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(results, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `zettel_suggest error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: zettel_converse\n// ---------------------------------------------------------------------------\n\nexport interface ZettelConverseParams {\n  question: string;\n  vault_project_id: number;\n  depth?: number;\n  limit?: number;\n}\n\nexport async function toolZettelConverse(\n  backend: StorageBackend,\n  params: ZettelConverseParams\n): Promise<ToolResult> {\n  try {\n    const { zettelConverse } = await import(\"../../zettelkasten/index.js\");\n    const result = await zettelConverse(backend, {\n      question: params.question,\n      vaultProjectId: params.vault_project_id,\n      depth: params.depth,\n      limit: params.limit,\n    });\n\n    // Query feedback loop: save query + result metadata for future indexing\n    try {\n      const { saveQueryResult } = await import(\"../../zettelkasten/query-feedback.js\");\n      saveQueryResult({\n        query: params.question,\n        timestamp: Date.now(),\n        source: \"zettel_converse\",\n        sourceSlugs: result.relevantNotes.slice(0, 5).map((n) => n.path),\n        answerPreview: result.relevantNotes.slice(0, 3).map((n) => {\n          const title = n.title ?? \"(untitled)\";\n          return `${title}: ${n.snippet.trim().slice(0, 100)}`;\n        }).join(\" | \"),\n        resultCount: result.relevantNotes.length,\n      });\n    } catch {\n      // Non-critical\n    }\n\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(result, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `zettel_converse error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: zettel_themes\n// ---------------------------------------------------------------------------\n\nexport interface ZettelThemesParams {\n  vault_project_id: number;\n  lookback_days?: number;\n  min_cluster_size?: number;\n  max_themes?: number;\n  similarity_threshold?: number;\n}\n\nexport async function toolZettelThemes(\n  backend: StorageBackend,\n  params: ZettelThemesParams\n): Promise<ToolResult> {\n  try {\n    const { zettelThemes } = await import(\"../../zettelkasten/index.js\");\n    const result = await zettelThemes(backend, {\n      vaultProjectId: params.vault_project_id,\n      lookbackDays: params.lookback_days,\n      minClusterSize: params.min_cluster_size,\n      maxThemes: params.max_themes,\n      similarityThreshold: params.similarity_threshold,\n    });\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(result, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `zettel_themes error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: zettel_god_notes\n// ---------------------------------------------------------------------------\n\nexport interface ZettelGodNotesParams {\n  limit?: number;\n  min_inbound?: number;\n}\n\nexport async function toolZettelGodNotes(\n  backend: StorageBackend,\n  params: ZettelGodNotesParams\n): Promise<ToolResult> {\n  try {\n    const { zettelGodNotes } = await import(\"../../zettelkasten/index.js\");\n    const result = await zettelGodNotes(backend, {\n      limit: params.limit,\n      minInbound: params.min_inbound,\n    });\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(result, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `zettel_god_notes error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: zettel_communities\n// ---------------------------------------------------------------------------\n\nexport interface ZettelCommunitiesParams {\n  min_size?: number;\n  max_communities?: number;\n  resolution?: number;\n}\n\nexport async function toolZettelCommunities(\n  backend: StorageBackend,\n  params: ZettelCommunitiesParams\n): Promise<ToolResult> {\n  try {\n    const { zettelCommunities } = await import(\"../../zettelkasten/index.js\");\n    const result = await zettelCommunities(backend, {\n      minSize: params.min_size,\n      maxCommunities: params.max_communities,\n      resolution: params.resolution,\n    });\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(result, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `zettel_communities error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n","/**\n * MCP tool handlers for the temporal knowledge graph.\n *\n * Tools:\n *   kg_add            — insert a new (subject, predicate, object) triple\n *   kg_query          — query triples with optional temporal filter\n *   kg_invalidate     — mark a triple as no longer valid (sets valid_to)\n *   kg_contradictions — find (subject, predicate) pairs with multiple valid objects\n */\n\nimport type { Pool } from \"pg\";\nimport type { ToolResult } from \"./types.js\";\nimport {\n  kgAdd,\n  kgQuery,\n  kgInvalidate,\n  kgContradictions,\n} from \"../../memory/kg.js\";\n\n// ---------------------------------------------------------------------------\n// Tool: kg_add\n// ---------------------------------------------------------------------------\n\nexport interface KgAddToolParams {\n  subject: string;\n  predicate: string;\n  object: string;\n  project_id?: number;\n  source_session?: string;\n  confidence?: \"EXTRACTED\" | \"INFERRED\" | \"AMBIGUOUS\";\n}\n\nexport async function toolKgAdd(\n  pool: Pool,\n  params: KgAddToolParams\n): Promise<ToolResult> {\n  try {\n    if (!params.subject || !params.predicate || !params.object) {\n      return {\n        content: [{ type: \"text\", text: \"kg_add error: subject, predicate, and object are required\" }],\n        isError: true,\n      };\n    }\n    const triple = await kgAdd(pool, params);\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(triple, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `kg_add error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: kg_query\n// ---------------------------------------------------------------------------\n\nexport interface KgQueryToolParams {\n  subject?: string;\n  predicate?: string;\n  object?: string;\n  project_id?: number;\n  as_of?: string; // ISO 8601 string; converted to Date\n  include_invalidated?: boolean;\n}\n\nexport async function toolKgQuery(\n  pool: Pool,\n  params: KgQueryToolParams\n): Promise<ToolResult> {\n  try {\n    const asOf = params.as_of ? new Date(params.as_of) : undefined;\n    if (asOf && isNaN(asOf.getTime())) {\n      return {\n        content: [{ type: \"text\", text: `kg_query error: invalid as_of date: ${params.as_of}` }],\n        isError: true,\n      };\n    }\n    const triples = await kgQuery(pool, {\n      subject: params.subject,\n      predicate: params.predicate,\n      object: params.object,\n      project_id: params.project_id,\n      as_of: asOf,\n      include_invalidated: params.include_invalidated,\n    });\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(triples, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `kg_query error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: kg_invalidate\n// ---------------------------------------------------------------------------\n\nexport interface KgInvalidateToolParams {\n  triple_id: number;\n}\n\nexport async function toolKgInvalidate(\n  pool: Pool,\n  params: KgInvalidateToolParams\n): Promise<ToolResult> {\n  try {\n    if (params.triple_id === undefined || params.triple_id === null) {\n      return {\n        content: [{ type: \"text\", text: \"kg_invalidate error: triple_id is required\" }],\n        isError: true,\n      };\n    }\n    await kgInvalidate(pool, params.triple_id);\n    return {\n      content: [{ type: \"text\", text: JSON.stringify({ invalidated: true, triple_id: params.triple_id }) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `kg_invalidate error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Tool: kg_contradictions\n// ---------------------------------------------------------------------------\n\nexport interface KgContradictionsToolParams {\n  subject: string;\n}\n\nexport async function toolKgContradictions(\n  pool: Pool,\n  params: KgContradictionsToolParams\n): Promise<ToolResult> {\n  try {\n    if (!params.subject) {\n      return {\n        content: [{ type: \"text\", text: \"kg_contradictions error: subject is required\" }],\n        isError: true,\n      };\n    }\n    const contradictions = await kgContradictions(pool, params.subject);\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(contradictions, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `kg_contradictions error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n","/**\n * Wake-up context system — progressive context loading inspired by mempalace.\n *\n * Layers:\n *   L0 Identity     (~100 tokens)   — user identity from ~/.pai/identity.txt. Always loaded.\n *   L1 Essential Story (~500-800t)  — top session notes for the project, key lines extracted.\n *   L2 On-Demand                    — triggered by topic queries (handled by memory_search).\n *   L3 Deep Search                  — unlimited federated memory search (memory_search tool).\n */\n\nimport { existsSync, readdirSync, readFileSync } from \"node:fs\";\nimport { join, basename } from \"node:path\";\nimport { homedir } from \"node:os\";\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Maximum tokens for the L1 essential story block. Approx 4 chars/token. */\nconst L1_TOKEN_BUDGET = 800;\nconst L1_CHAR_BUDGET = L1_TOKEN_BUDGET * 4; // ~3200 chars\n\n/** Maximum session notes to scan when building L1. */\nconst L1_MAX_NOTES = 10;\n\n/** Sections to extract from session notes (in priority order). */\nconst EXTRACT_SECTIONS = [\n  \"Work Done\",\n  \"Key Decisions\",\n  \"Next Steps\",\n  \"Checkpoint\",\n];\n\n/** Identity file location. */\nconst IDENTITY_FILE = join(homedir(), \".pai\", \"identity.txt\");\n\n// ---------------------------------------------------------------------------\n// L0: Identity\n// ---------------------------------------------------------------------------\n\n/**\n * Load L0 identity from ~/.pai/identity.txt.\n * Returns the file content, or an empty string if the file does not exist.\n * Never throws.\n */\nexport function loadL0Identity(): string {\n  if (!existsSync(IDENTITY_FILE)) return \"\";\n  try {\n    return readFileSync(IDENTITY_FILE, \"utf-8\").trim();\n  } catch {\n    return \"\";\n  }\n}\n\n// ---------------------------------------------------------------------------\n// L1: Essential Story\n// ---------------------------------------------------------------------------\n\n/**\n * Find the Notes directory for a project given its root_path from the registry.\n * Checks local Notes/ first, then central ~/.claude/projects/... path.\n */\nfunction findNotesDirForProject(rootPath: string): string | null {\n  // Check local Notes directories first\n  const localCandidates = [\n    join(rootPath, \"Notes\"),\n    join(rootPath, \"notes\"),\n    join(rootPath, \".claude\", \"Notes\"),\n  ];\n  for (const p of localCandidates) {\n    if (existsSync(p)) return p;\n  }\n\n  // Fall back to central ~/.claude/projects/{encoded}/Notes\n  const encoded = rootPath\n    .replace(/\\//g, \"-\")\n    .replace(/\\./g, \"-\")\n    .replace(/ /g, \"-\");\n  const centralNotes = join(\n    homedir(),\n    \".claude\",\n    \"projects\",\n    encoded,\n    \"Notes\"\n  );\n  if (existsSync(centralNotes)) return centralNotes;\n\n  return null;\n}\n\n/**\n * Recursively find all .md session note files in a Notes directory.\n * Handles both flat layout (Notes/*.md) and month-subdirectory layout\n * (Notes/YYYY/MM/*.md). Returns files sorted newest-first by filename\n * (note numbers are monotonically increasing, so lexicographic = newest-last,\n * so we reverse).\n */\nfunction findSessionNotes(notesDir: string): string[] {\n  const result: string[] = [];\n\n  const scanDir = (dir: string) => {\n    if (!existsSync(dir)) return;\n    let entries: string[];\n    try {\n      entries = readdirSync(dir, { withFileTypes: true } as Parameters<typeof readdirSync>[1] as any)\n        .map((e: any) => ({ name: e.name, isDir: e.isDirectory() }));\n    } catch {\n      return;\n    }\n\n    for (const entry of entries as Array<{ name: string; isDir: boolean }>) {\n      const fullPath = join(dir, entry.name);\n      if (entry.isDir) {\n        // Recurse into YYYY/MM subdirectories\n        scanDir(fullPath);\n      } else if (entry.name.match(/^\\d{3,4}[\\s_-].*\\.md$/)) {\n        result.push(fullPath);\n      }\n    }\n  };\n\n  scanDir(notesDir);\n\n  // Sort: extract leading number, highest = most recent\n  result.sort((a, b) => {\n    const numA = parseInt(basename(a).match(/^(\\d+)/)?.[1] ?? \"0\", 10);\n    const numB = parseInt(basename(b).match(/^(\\d+)/)?.[1] ?? \"0\", 10);\n    return numB - numA; // newest first\n  });\n\n  return result;\n}\n\n/**\n * Extract the most important lines from a session note.\n * Prioritises: Work Done items, Key Decisions, Next Steps, Checkpoint headings.\n * Returns a condensed string under maxChars.\n */\nfunction extractKeyLines(content: string, maxChars: number): string {\n  const lines = content.split(\"\\n\");\n  const selected: string[] = [];\n  let inTargetSection = false;\n  let currentSection = \"\";\n  let charCount = 0;\n\n  // First pass: collect lines from priority sections\n  for (const line of lines) {\n    // Detect section headers\n    const h2Match = line.match(/^## (.+)$/);\n    const h3Match = line.match(/^### (.+)$/);\n    if (h2Match) {\n      currentSection = h2Match[1];\n      inTargetSection = EXTRACT_SECTIONS.some((s) =>\n        currentSection.toLowerCase().includes(s.toLowerCase())\n      );\n      continue;\n    }\n    if (h3Match) {\n      // Checkpoints / sub-sections — include heading as label\n      if (inTargetSection) {\n        const label = `[${h3Match[1]}]`;\n        if (charCount + label.length < maxChars) {\n          selected.push(label);\n          charCount += label.length + 1;\n        }\n      }\n      continue;\n    }\n\n    if (!inTargetSection) continue;\n\n    // Skip blank lines and HTML comments\n    const trimmed = line.trim();\n    if (!trimmed || trimmed.startsWith(\"<!--\") || trimmed === \"---\") continue;\n\n    // Include checkbox items, bold text, and plain text lines\n    if (\n      trimmed.startsWith(\"- \") ||\n      trimmed.startsWith(\"* \") ||\n      trimmed.match(/^\\d+\\./) ||\n      trimmed.startsWith(\"**\")\n    ) {\n      if (charCount + trimmed.length + 1 > maxChars) break;\n      selected.push(trimmed);\n      charCount += trimmed.length + 1;\n    }\n  }\n\n  return selected.join(\"\\n\");\n}\n\n/**\n * Build the L1 essential story block.\n *\n * Reads the most recent session notes for the project and extracts the key\n * lines (Work Done, Key Decisions, Next Steps) within the token budget.\n *\n * @param rootPath   The project root path (from the registry).\n * @param tokenBudget  Max tokens to consume. Default 800 (~3200 chars).\n * @returns Formatted L1 block, or empty string if no notes found.\n */\nexport function buildL1EssentialStory(\n  rootPath: string,\n  tokenBudget = L1_TOKEN_BUDGET\n): string {\n  const charBudget = tokenBudget * 4;\n  const notesDir = findNotesDirForProject(rootPath);\n  if (!notesDir) return \"\";\n\n  const noteFiles = findSessionNotes(notesDir).slice(0, L1_MAX_NOTES);\n  if (noteFiles.length === 0) return \"\";\n\n  const sections: string[] = [];\n  let remaining = charBudget;\n\n  for (const noteFile of noteFiles) {\n    if (remaining <= 50) break;\n\n    let content: string;\n    try {\n      content = readFileSync(noteFile, \"utf-8\");\n    } catch {\n      continue;\n    }\n\n    // Extract the note date and title from the filename\n    const name = basename(noteFile);\n    const titleMatch = name.match(/^\\d+ - (\\d{4}-\\d{2}-\\d{2}) - (.+)\\.md$/);\n    const dateLabel = titleMatch ? titleMatch[1] : \"\";\n    const titleLabel = titleMatch\n      ? titleMatch[2]\n      : name.replace(/^\\d+ - /, \"\").replace(/\\.md$/, \"\");\n\n    // Skip if nothing useful extracted from this note\n    const perNoteChars = Math.min(remaining, Math.floor(charBudget / noteFiles.length) + 200);\n    const extracted = extractKeyLines(content, perNoteChars);\n    if (!extracted) continue;\n\n    const noteBlock = `[${dateLabel} - ${titleLabel}]\\n${extracted}`;\n    sections.push(noteBlock);\n    remaining -= noteBlock.length + 1;\n  }\n\n  if (sections.length === 0) return \"\";\n\n  return sections.join(\"\\n\\n\");\n}\n\n// ---------------------------------------------------------------------------\n// Combined: buildWakeupContext\n// ---------------------------------------------------------------------------\n\n/**\n * Build the combined wake-up context block (L0 + L1).\n *\n * Returns a formatted string suitable for injection as a system-reminder,\n * or an empty string if both layers are empty.\n *\n * @param rootPath   Project root path for L1 note lookup. Optional.\n * @param tokenBudget  L1 token budget. Default 800.\n */\nexport function buildWakeupContext(\n  rootPath?: string,\n  tokenBudget = L1_TOKEN_BUDGET\n): string {\n  const identity = loadL0Identity();\n  const essentialStory = rootPath\n    ? buildL1EssentialStory(rootPath, tokenBudget)\n    : \"\";\n\n  if (!identity && !essentialStory) return \"\";\n\n  const parts: string[] = [];\n\n  if (identity) {\n    parts.push(`## L0 Identity\\n\\n${identity}`);\n  }\n\n  if (essentialStory) {\n    parts.push(`## L1 Essential Story\\n\\n${essentialStory}`);\n  }\n\n  return parts.join(\"\\n\\n\");\n}\n","/**\n * MCP tool handler: memory_wakeup\n *\n * Returns the L0+L1 wake-up context block for a project:\n *   L0 — user identity from ~/.pai/identity.txt\n *   L1 — recent session note highlights (Work Done / Key Decisions / Next Steps)\n */\n\nimport type { Database } from \"better-sqlite3\";\nimport { buildWakeupContext } from \"../../memory/wakeup.js\";\nimport { detectProjectFromPath } from \"./types.js\";\nimport type { ToolResult } from \"./types.js\";\n\n// ---------------------------------------------------------------------------\n// Default token budget (constant, overridable per call)\n// ---------------------------------------------------------------------------\n\nconst DEFAULT_TOKEN_BUDGET = 800;\n\n// ---------------------------------------------------------------------------\n// Params\n// ---------------------------------------------------------------------------\n\nexport interface MemoryWakeupParams {\n  /** Project slug or absolute path. Omit to auto-detect from process.cwd(). */\n  project?: string;\n  /** L1 token budget. Default 800. */\n  token_budget?: number;\n}\n\n// ---------------------------------------------------------------------------\n// Tool handler\n// ---------------------------------------------------------------------------\n\nexport function toolMemoryWakeup(\n  registryDb: Database,\n  params: MemoryWakeupParams\n): ToolResult {\n  try {\n    const tokenBudget = params.token_budget ?? DEFAULT_TOKEN_BUDGET;\n\n    // Resolve the project root path\n    let rootPath: string | undefined;\n\n    if (params.project) {\n      // Try slug lookup first\n      const bySlug = registryDb\n        .prepare(\"SELECT root_path FROM projects WHERE slug = ?\")\n        .get(params.project) as { root_path: string } | undefined;\n\n      if (bySlug) {\n        rootPath = bySlug.root_path;\n      } else {\n        // Maybe it's an absolute path — try path-based detect\n        const detected = detectProjectFromPath(registryDb, params.project);\n        if (detected) rootPath = detected.root_path;\n      }\n    } else {\n      // Auto-detect from cwd\n      const detected = detectProjectFromPath(registryDb, process.cwd());\n      if (detected) rootPath = detected.root_path;\n    }\n\n    const wakeupBlock = buildWakeupContext(rootPath, tokenBudget);\n\n    if (!wakeupBlock) {\n      return {\n        content: [\n          {\n            type: \"text\",\n            text: \"No wake-up context available. Create ~/.pai/identity.txt for L0 identity, or ensure session notes exist for L1 story.\",\n          },\n        ],\n      };\n    }\n\n    return {\n      content: [\n        {\n          type: \"text\",\n          text: `WAKEUP CONTEXT\\n\\n${wakeupBlock}`,\n        },\n      ],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `Wakeup context error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n","/**\n * getTaxonomy — returns the shape of stored memory without requiring a query.\n *\n * Answers \"what do I know about?\" not \"what do I know about X?\"\n *\n * Uses the registry DB (projects, sessions) and the storage backend\n * (memory_files, memory_chunks) to build a structural overview.\n */\n\nimport type { Database } from \"better-sqlite3\";\nimport type { StorageBackend } from \"../storage/interface.js\";\n\n// ---------------------------------------------------------------------------\n// Return types\n// ---------------------------------------------------------------------------\n\nexport interface TaxonomyProject {\n  slug: string;\n  display_name: string;\n  session_count: number;\n  note_count: number;\n  last_activity: string | null; // ISO date string, e.g. \"2026-04-07\"\n  top_tags: string[];            // project tags from the registry\n}\n\nexport interface TaxonomyTotals {\n  projects: number;\n  sessions: number;\n  notes: number;\n  chunks: number;\n}\n\nexport interface TaxonomyRecentActivity {\n  project_slug: string;\n  action: string;\n  timestamp: string; // ISO date string\n}\n\nexport interface TaxonomyResult {\n  projects: TaxonomyProject[];\n  totals: TaxonomyTotals;\n  recent_activity: TaxonomyRecentActivity[];\n}\n\n// ---------------------------------------------------------------------------\n// Options\n// ---------------------------------------------------------------------------\n\nexport interface TaxonomyOptions {\n  /** Include archived projects. Default: false. */\n  include_archived?: boolean;\n  /** Maximum projects to return. Default: 50. */\n  limit?: number;\n}\n\n// ---------------------------------------------------------------------------\n// Main function\n// ---------------------------------------------------------------------------\n\n/**\n * Build a taxonomy of stored memory — what projects exist, how much is stored,\n * and what has been active recently.\n *\n * Registry queries (projects, sessions) are synchronous (better-sqlite3).\n * Storage backend queries (files, chunks) are async.\n */\nexport async function getTaxonomy(\n  registryDb: Database,\n  storage: StorageBackend,\n  options: TaxonomyOptions = {}\n): Promise<TaxonomyResult> {\n  const includeArchived = options.include_archived ?? false;\n  const limit = options.limit ?? 50;\n\n  // -------------------------------------------------------------------------\n  // 1. Load all (active) projects from the registry\n  // -------------------------------------------------------------------------\n\n  const statusFilter = includeArchived\n    ? \"status IN ('active', 'archived', 'migrating')\"\n    : \"status = 'active'\";\n\n  const projectRows = registryDb\n    .prepare(\n      `SELECT id, slug, display_name, status, created_at, updated_at\n       FROM projects\n       WHERE ${statusFilter}\n       ORDER BY updated_at DESC\n       LIMIT ?`\n    )\n    .all(limit) as Array<{\n    id: number;\n    slug: string;\n    display_name: string;\n    status: string;\n    created_at: number;\n    updated_at: number;\n  }>;\n\n  if (projectRows.length === 0) {\n    return {\n      projects: [],\n      totals: { projects: 0, sessions: 0, notes: 0, chunks: 0 },\n      recent_activity: [],\n    };\n  }\n\n  const projectIds = projectRows.map((p) => p.id);\n\n  // -------------------------------------------------------------------------\n  // 2. Session counts per project (registry, synchronous)\n  // -------------------------------------------------------------------------\n\n  const sessionCountsByProject = new Map<number, number>();\n  const lastSessionDateByProject = new Map<number, string | null>();\n\n  for (const projectId of projectIds) {\n    const countRow = registryDb\n      .prepare(\"SELECT COUNT(*) AS n FROM sessions WHERE project_id = ?\")\n      .get(projectId) as { n: number };\n    sessionCountsByProject.set(projectId, countRow.n);\n\n    const lastRow = registryDb\n      .prepare(\n        \"SELECT date FROM sessions WHERE project_id = ? ORDER BY number DESC LIMIT 1\"\n      )\n      .get(projectId) as { date: string } | undefined;\n    lastSessionDateByProject.set(projectId, lastRow?.date ?? null);\n  }\n\n  // -------------------------------------------------------------------------\n  // 3. Tags per project (registry, synchronous)\n  // -------------------------------------------------------------------------\n\n  const tagsByProject = new Map<number, string[]>();\n\n  for (const projectId of projectIds) {\n    const tags = registryDb\n      .prepare(\n        `SELECT t.name\n         FROM tags t\n         JOIN project_tags pt ON pt.tag_id = t.id\n         WHERE pt.project_id = ?\n         ORDER BY t.name`\n      )\n      .all(projectId) as Array<{ name: string }>;\n    tagsByProject.set(projectId, tags.map((t) => t.name));\n  }\n\n  // -------------------------------------------------------------------------\n  // 4. Note and chunk counts per project (storage backend, async)\n  //    We use memory_files for note count (one row per indexed file) and\n  //    memory_chunks for chunk count (may be many per file).\n  //    The StorageBackend interface exposes getStats() for totals but not\n  //    per-project breakdowns, so we cast to the raw DB when it is SQLite\n  //    and fall back to a single getStats() call for Postgres.\n  // -------------------------------------------------------------------------\n\n  const noteCountsByProject = new Map<number, number>();\n  const chunkCountsByProject = new Map<number, number>();\n\n  const isBackend = (x: StorageBackend): boolean => x.backendType === \"sqlite\";\n\n  if (isBackend(storage)) {\n    // SQLite: access raw DB via the getRawDb() escape hatch present on SQLiteBackend.\n    // We reach through the interface via a duck-type check — getRawDb is not on the\n    // interface but is documented as an escape hatch for exactly this kind of work.\n    const rawDb = (storage as unknown as { getRawDb?: () => Database }).getRawDb?.();\n    if (rawDb) {\n      for (const projectId of projectIds) {\n        const noteRow = rawDb\n          .prepare(\n            \"SELECT COUNT(*) AS n FROM memory_files WHERE project_id = ?\"\n          )\n          .get(projectId) as { n: number };\n        noteCountsByProject.set(projectId, noteRow.n);\n\n        const chunkRow = rawDb\n          .prepare(\n            \"SELECT COUNT(*) AS n FROM memory_chunks WHERE project_id = ?\"\n          )\n          .get(projectId) as { n: number };\n        chunkCountsByProject.set(projectId, chunkRow.n);\n      }\n    }\n  } else {\n    // Postgres: the storage backend interface does not expose per-project file/chunk\n    // counts, so we leave them as 0 — totals are still reported via getStats().\n    // Future: add per-project getStats(projectId?) to the interface if needed.\n    for (const projectId of projectIds) {\n      noteCountsByProject.set(projectId, 0);\n      chunkCountsByProject.set(projectId, 0);\n    }\n  }\n\n  // -------------------------------------------------------------------------\n  // 5. Global totals\n  // -------------------------------------------------------------------------\n\n  const stats = await storage.getStats();\n\n  const totalProjects = (\n    registryDb\n      .prepare(\n        `SELECT COUNT(*) AS n FROM projects WHERE ${statusFilter}`\n      )\n      .get() as { n: number }\n  ).n;\n\n  const totalSessions = (\n    registryDb.prepare(\"SELECT COUNT(*) AS n FROM sessions\").get() as { n: number }\n  ).n;\n\n  // -------------------------------------------------------------------------\n  // 6. Recent activity — last 10 sessions across all projects\n  // -------------------------------------------------------------------------\n\n  const recentSessions = registryDb\n    .prepare(\n      `SELECT s.date, s.title, p.slug\n       FROM sessions s\n       JOIN projects p ON p.id = s.project_id\n       WHERE p.${statusFilter.replace(\"status\", \"p.status\")}\n       ORDER BY s.created_at DESC\n       LIMIT 10`\n    )\n    .all() as Array<{ date: string; title: string; slug: string }>;\n\n  const recentActivity: TaxonomyRecentActivity[] = recentSessions.map((row) => ({\n    project_slug: row.slug,\n    action: `session: ${row.title || \"(untitled)\"}`,\n    timestamp: row.date,\n  }));\n\n  // -------------------------------------------------------------------------\n  // 7. Assemble result\n  // -------------------------------------------------------------------------\n\n  const projects: TaxonomyProject[] = projectRows.map((row) => ({\n    slug: row.slug,\n    display_name: row.display_name,\n    session_count: sessionCountsByProject.get(row.id) ?? 0,\n    note_count: noteCountsByProject.get(row.id) ?? 0,\n    last_activity: lastSessionDateByProject.get(row.id) ?? null,\n    top_tags: tagsByProject.get(row.id) ?? [],\n  }));\n\n  return {\n    projects,\n    totals: {\n      projects: totalProjects,\n      sessions: totalSessions,\n      notes: stats.files,\n      chunks: stats.chunks,\n    },\n    recent_activity: recentActivity,\n  };\n}\n","/**\n * MCP tool handler: memory_taxonomy\n *\n * Returns the SHAPE of stored memory without requiring a query.\n * Answers \"what do I know about?\" not \"what do I know about X?\"\n */\n\nimport type { Database } from \"better-sqlite3\";\nimport type { StorageBackend } from \"../../storage/interface.js\";\nimport { getTaxonomy } from \"../../memory/taxonomy.js\";\nimport type { ToolResult } from \"./types.js\";\n\n// ---------------------------------------------------------------------------\n// Tool: memory_taxonomy\n// ---------------------------------------------------------------------------\n\nexport interface MemoryTaxonomyParams {\n  /** Include archived projects in the result. Default: false. */\n  include_archived?: boolean;\n  /** Maximum number of projects to return. Default: 50. */\n  limit?: number;\n}\n\nexport async function toolMemoryTaxonomy(\n  registryDb: Database,\n  storage: StorageBackend,\n  params: MemoryTaxonomyParams = {}\n): Promise<ToolResult> {\n  try {\n    const result = await getTaxonomy(registryDb, storage, {\n      include_archived: params.include_archived,\n      limit: params.limit,\n    });\n\n    // -----------------------------------------------------------------------\n    // Format output as human-readable text\n    // -----------------------------------------------------------------------\n\n    const lines: string[] = [];\n\n    // Totals header\n    lines.push(\n      `PAI Memory Taxonomy — ${result.totals.projects} project(s), ` +\n        `${result.totals.sessions} session(s), ` +\n        `${result.totals.notes} indexed file(s), ` +\n        `${result.totals.chunks} chunk(s)`\n    );\n    lines.push(\"\");\n\n    // Per-project breakdown\n    if (result.projects.length === 0) {\n      lines.push(\"No active projects found.\");\n    } else {\n      lines.push(\"Projects:\");\n      for (const p of result.projects) {\n        const tagStr = p.top_tags.length > 0 ? ` [${p.top_tags.join(\", \")}]` : \"\";\n        const activityStr = p.last_activity ? ` last: ${p.last_activity}` : \"\";\n        lines.push(\n          `  ${p.slug} — ${p.display_name}` +\n            `  sessions=${p.session_count}` +\n            (p.note_count > 0 ? ` files=${p.note_count}` : \"\") +\n            activityStr +\n            tagStr\n        );\n      }\n    }\n\n    // Recent activity\n    if (result.recent_activity.length > 0) {\n      lines.push(\"\");\n      lines.push(\"Recent activity (last 10 sessions across all projects):\");\n      for (const a of result.recent_activity) {\n        lines.push(`  ${a.timestamp}  ${a.project_slug}  ${a.action}`);\n      }\n    }\n\n    return {\n      content: [{ type: \"text\", text: lines.join(\"\\n\") }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `memory_taxonomy error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n","/**\n * tunnels.ts — cross-project concept detection (\"palace graph / tunnel detection\")\n *\n * A \"tunnel\" is a concept (word or short phrase) that appears in chunks from\n * at least two distinct projects.  These serendipitous cross-project connections\n * are surfaced so the user can discover unexpected relationships between their\n * work streams.\n *\n * Algorithm:\n *  1. Pull the top-N most frequent significant terms from memory_chunks via BM25 FTS.\n *     We use the FTS5 vocab table (if available) or fall back to term frequency\n *     aggregation over the raw text via a trigram approach.\n *  2. For each candidate term, count how many distinct projects have at least one\n *     chunk containing it and aggregate occurrence stats.\n *  3. Filter by min_projects and min_occurrences, sort by project breadth then\n *     frequency, return top limit results.\n *\n * Backend support:\n *  - SQLite  — uses `memory_fts` MATCH to count per-project occurrences.\n *  - Postgres — uses `memory_chunks` tsvector + ts_stat for term extraction and\n *               per-project term frequency counting via plainto_tsquery.\n */\n\nimport { STOP_WORDS } from \"../utils/stop-words.js\";\nimport type { StorageBackend } from \"../storage/interface.js\";\n\n// ---------------------------------------------------------------------------\n// Public types\n// ---------------------------------------------------------------------------\n\nexport interface Tunnel {\n  /** The shared term or phrase. */\n  concept: string;\n  /** Project slugs where this concept appears. */\n  projects: string[];\n  /** Total chunk occurrences across all projects. */\n  occurrences: number;\n  /** First time the concept appeared (Unix ms). */\n  first_seen: number;\n  /** Most recent time the concept appeared (Unix ms). */\n  last_seen: number;\n}\n\nexport interface FindTunnelsOptions {\n  /** Minimum distinct projects a concept must appear in. Default 2. */\n  min_projects?: number;\n  /** Minimum total chunk occurrences across all projects. Default 3. */\n  min_occurrences?: number;\n  /** Maximum number of tunnels to return. Default 20. */\n  limit?: number;\n}\n\nexport interface FindTunnelsResult {\n  tunnels: Tunnel[];\n  projects_analyzed: number;\n  total_concepts_evaluated: number;\n}\n\n// ---------------------------------------------------------------------------\n// Internal row types\n// ---------------------------------------------------------------------------\n\ninterface ProjectSlugMap {\n  [id: number]: string;\n}\n\n// ---------------------------------------------------------------------------\n// SQLite implementation\n// ---------------------------------------------------------------------------\n\n/**\n * Extract candidate terms from the SQLite FTS5 index using the vocabulary\n * approach: iterate the fts5vocab table (if it exists) for the most common\n * terms, then per-term count distinct projects.\n */\nasync function findTunnelsSqlite(\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  db: any,\n  slugMap: ProjectSlugMap,\n  opts: Required<FindTunnelsOptions>\n): Promise<FindTunnelsResult> {\n  const projectIds = Object.keys(slugMap).map(Number);\n  if (projectIds.length < 2) {\n    return { tunnels: [], projects_analyzed: projectIds.length, total_concepts_evaluated: 0 };\n  }\n\n  // Step 1 — collect candidate terms via FTS5 vocabulary shadow table.\n  // memory_fts uses the standard fts5 content table; the vocab view is\n  // \"memory_fts_v\" if it was created, otherwise we fall back to sampling.\n  let candidateTerms: string[] = [];\n\n  try {\n    // fts5vocab \"col\" mode: (term, col, doc, cnt) — aggregate all cols.\n    const vocabRows = db\n      .prepare(\n        `SELECT term, SUM(doc) AS doc_count, SUM(cnt) AS total_cnt\n         FROM memory_fts_v\n         GROUP BY term\n         HAVING SUM(cnt) >= ?\n         ORDER BY SUM(doc) DESC\n         LIMIT 500`\n      )\n      .all(opts.min_occurrences) as Array<{ term: string; doc_count: number; total_cnt: number }>;\n\n    candidateTerms = vocabRows\n      .map((r) => r.term)\n      .filter((t) => t.length >= 3 && !STOP_WORDS.has(t));\n  } catch {\n    // Vocab table not available — fall back to sampling common words from chunks.\n    // We aggregate word tokens from a sample of chunks using SQLite string ops.\n    // This is slower but works on any SQLite federation.db.\n    const sampleRows = db\n      .prepare(\n        `SELECT LOWER(text) AS text FROM memory_chunks\n         WHERE LENGTH(text) > 20\n         ORDER BY RANDOM()\n         LIMIT 2000`\n      )\n      .all() as Array<{ text: string }>;\n\n    const freq = new Map<string, number>();\n    for (const { text } of sampleRows) {\n      const tokens = text\n        .split(/[\\s\\p{P}]+/u)\n        .filter(Boolean)\n        .filter((t: string) => t.length >= 3 && !STOP_WORDS.has(t));\n      for (const t of tokens) {\n        freq.set(t, (freq.get(t) ?? 0) + 1);\n      }\n    }\n    candidateTerms = [...freq.entries()]\n      .filter(([, n]) => n >= opts.min_occurrences)\n      .sort((a, b) => b[1] - a[1])\n      .slice(0, 200)\n      .map(([t]) => t);\n  }\n\n  if (candidateTerms.length === 0) {\n    return { tunnels: [], projects_analyzed: projectIds.length, total_concepts_evaluated: 0 };\n  }\n\n  // Step 2 — for each candidate, count distinct projects and occurrences.\n  const tunnels: Tunnel[] = [];\n\n  for (const term of candidateTerms) {\n    try {\n      const rows = db\n        .prepare(\n          `SELECT c.project_id, COUNT(*) AS cnt,\n                  MIN(c.updated_at) AS first_seen,\n                  MAX(c.updated_at) AS last_seen\n           FROM memory_fts f\n           JOIN memory_chunks c ON c.id = f.id\n           WHERE memory_fts MATCH ?\n             AND c.project_id IN (${projectIds.map(() => \"?\").join(\", \")})\n           GROUP BY c.project_id`\n        )\n        .all(`\"${term.replace(/\"/g, '\"\"')}\"`, ...projectIds) as Array<{\n          project_id: number;\n          cnt: number;\n          first_seen: number;\n          last_seen: number;\n        }>;\n\n      if (rows.length < opts.min_projects) continue;\n\n      const totalOccurrences = rows.reduce((s, r) => s + Number(r.cnt), 0);\n      if (totalOccurrences < opts.min_occurrences) continue;\n\n      const projects = rows\n        .map((r) => slugMap[r.project_id] ?? String(r.project_id))\n        .filter(Boolean);\n      const firstSeen = Math.min(...rows.map((r) => r.first_seen));\n      const lastSeen = Math.max(...rows.map((r) => r.last_seen));\n\n      tunnels.push({\n        concept: term,\n        projects,\n        occurrences: totalOccurrences,\n        first_seen: firstSeen,\n        last_seen: lastSeen,\n      });\n    } catch {\n      // Skip problematic terms\n      continue;\n    }\n  }\n\n  // Sort: most cross-project spread first, then by raw frequency.\n  tunnels.sort((a, b) => {\n    const byProjects = b.projects.length - a.projects.length;\n    if (byProjects !== 0) return byProjects;\n    return b.occurrences - a.occurrences;\n  });\n\n  return {\n    tunnels: tunnels.slice(0, opts.limit),\n    projects_analyzed: projectIds.length,\n    total_concepts_evaluated: candidateTerms.length,\n  };\n}\n\n// ---------------------------------------------------------------------------\n// Postgres implementation\n// ---------------------------------------------------------------------------\n\n/**\n * Use Postgres ts_stat() + plainto_tsquery to efficiently find terms that\n * appear across multiple projects.\n */\nasync function findTunnelsPostgres(\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  pool: any,\n  slugMap: ProjectSlugMap,\n  opts: Required<FindTunnelsOptions>\n): Promise<FindTunnelsResult> {\n  const projectIds = Object.keys(slugMap).map(Number);\n  if (projectIds.length < 2) {\n    return { tunnels: [], projects_analyzed: projectIds.length, total_concepts_evaluated: 0 };\n  }\n\n  // Step 1 — extract top terms from the corpus using ts_stat over all chunks.\n  // ts_stat(query) returns (word, ndoc, nentry) for each lexeme in the tsvector.\n  const termResult = await pool.query<{ word: string; ndoc: string; nentry: string }>(\n    `SELECT word, ndoc, nentry\n     FROM ts_stat(\n       'SELECT to_tsvector(''simple'', text) FROM memory_chunks WHERE project_id = ANY($1)'\n     )\n     WHERE length(word) >= 3\n       AND nentry >= $2\n     ORDER BY ndoc DESC\n     LIMIT 500`,\n    [projectIds, opts.min_occurrences]\n  );\n\n  let candidateTerms = termResult.rows\n    .map((r) => r.word)\n    .filter((t) => !STOP_WORDS.has(t));\n\n  if (candidateTerms.length === 0) {\n    return { tunnels: [], projects_analyzed: projectIds.length, total_concepts_evaluated: 0 };\n  }\n\n  // Cap at 200 candidates for performance.\n  candidateTerms = candidateTerms.slice(0, 200);\n\n  // Step 2 — for each candidate, count distinct projects via a single batched query.\n  // We use a VALUES list + JOIN to avoid N+1 round-trips.\n  const valuesClause = candidateTerms\n    .map((t, i) => `($${i + 2}::text)`)\n    .join(\", \");\n\n  const batchResult = await pool.query<{\n    concept: string;\n    project_id: string;\n    cnt: string;\n    first_seen: string;\n    last_seen: string;\n  }>(\n    `SELECT v.concept, c.project_id::text, COUNT(*) AS cnt,\n            MIN(c.updated_at) AS first_seen,\n            MAX(c.updated_at) AS last_seen\n     FROM (VALUES ${valuesClause}) AS v(concept)\n     JOIN memory_chunks c\n       ON to_tsvector('simple', c.text) @@ plainto_tsquery('simple', v.concept)\n      AND c.project_id = ANY($1)\n     GROUP BY v.concept, c.project_id`,\n    [projectIds, ...candidateTerms]\n  );\n\n  // Aggregate by concept.\n  const byConceptMap = new Map<\n    string,\n    { projects: Set<number>; occurrences: number; firstSeen: number; lastSeen: number }\n  >();\n\n  for (const row of batchResult.rows) {\n    const existing = byConceptMap.get(row.concept) ?? {\n      projects: new Set<number>(),\n      occurrences: 0,\n      firstSeen: Infinity,\n      lastSeen: -Infinity,\n    };\n    existing.projects.add(parseInt(row.project_id, 10));\n    existing.occurrences += parseInt(row.cnt, 10);\n    const fs = parseInt(row.first_seen, 10);\n    const ls = parseInt(row.last_seen, 10);\n    if (fs < existing.firstSeen) existing.firstSeen = fs;\n    if (ls > existing.lastSeen) existing.lastSeen = ls;\n    byConceptMap.set(row.concept, existing);\n  }\n\n  const tunnels: Tunnel[] = [];\n  for (const [concept, data] of byConceptMap) {\n    if (data.projects.size < opts.min_projects) continue;\n    if (data.occurrences < opts.min_occurrences) continue;\n\n    const projects = [...data.projects]\n      .map((id) => slugMap[id] ?? String(id))\n      .filter(Boolean);\n\n    tunnels.push({\n      concept,\n      projects,\n      occurrences: data.occurrences,\n      first_seen: data.firstSeen === Infinity ? 0 : data.firstSeen,\n      last_seen: data.lastSeen === -Infinity ? 0 : data.lastSeen,\n    });\n  }\n\n  tunnels.sort((a, b) => {\n    const byProjects = b.projects.length - a.projects.length;\n    if (byProjects !== 0) return byProjects;\n    return b.occurrences - a.occurrences;\n  });\n\n  return {\n    tunnels: tunnels.slice(0, opts.limit),\n    projects_analyzed: projectIds.length,\n    total_concepts_evaluated: candidateTerms.length,\n  };\n}\n\n// ---------------------------------------------------------------------------\n// Public entry point\n// ---------------------------------------------------------------------------\n\n/**\n * Find cross-project concept tunnels.\n *\n * Works with both SQLite and Postgres storage backends.\n * Requires the `registryDb` (better-sqlite3) for project slug resolution.\n *\n * @param backend        Active PAI storage backend.\n * @param registryDb     Registry database for project slug resolution.\n * @param options        Filter and limit options.\n */\nexport async function findTunnels(\n  backend: StorageBackend,\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  registryDb: any,\n  options?: FindTunnelsOptions\n): Promise<FindTunnelsResult> {\n  const opts: Required<FindTunnelsOptions> = {\n    min_projects: options?.min_projects ?? 2,\n    min_occurrences: options?.min_occurrences ?? 3,\n    limit: options?.limit ?? 20,\n  };\n\n  // Build project slug map from registry.\n  const projectRows = registryDb\n    .prepare(\"SELECT id, slug FROM projects WHERE status != 'archived'\")\n    .all() as Array<{ id: number; slug: string }>;\n\n  const slugMap: ProjectSlugMap = {};\n  for (const { id, slug } of projectRows) {\n    slugMap[id] = slug;\n  }\n\n  if (backend.backendType === \"postgres\") {\n    // eslint-disable-next-line @typescript-eslint/no-explicit-any\n    const pool = (backend as any).getPool?.();\n    if (!pool) {\n      throw new Error(\"findTunnels: Postgres backend does not expose getPool()\");\n    }\n    return findTunnelsPostgres(pool, slugMap, opts);\n  }\n\n  // SQLite path — access raw db through the backend adapter.\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  const rawDb = (backend as any).getRawDb?.();\n  if (!rawDb) {\n    throw new Error(\"findTunnels: SQLite backend does not expose getRawDb()\");\n  }\n  return findTunnelsSqlite(rawDb, slugMap, opts);\n}\n","/**\n * MCP tool handler: memory_tunnels\n *\n * Finds \"tunnels\" — concepts that appear across multiple projects —\n * surfacing cross-project serendipitous connections in the PAI memory graph.\n */\n\nimport type { Database } from \"better-sqlite3\";\nimport type { StorageBackend } from \"../../storage/interface.js\";\nimport type { ToolResult } from \"./types.js\";\nimport { findTunnels } from \"../../memory/tunnels.js\";\n\n// ---------------------------------------------------------------------------\n// Tool: memory_tunnels\n// ---------------------------------------------------------------------------\n\nexport interface MemoryTunnelsParams {\n  /** Minimum distinct projects a concept must appear in. Default 2. */\n  min_projects?: number;\n  /** Minimum total chunk occurrences across all projects. Default 3. */\n  min_occurrences?: number;\n  /** Maximum number of tunnels to return. Default 20. */\n  limit?: number;\n}\n\nexport async function toolMemoryTunnels(\n  registryDb: Database,\n  backend: StorageBackend,\n  params: MemoryTunnelsParams\n): Promise<ToolResult> {\n  try {\n    const result = await findTunnels(backend, registryDb, {\n      min_projects: params.min_projects,\n      min_occurrences: params.min_occurrences,\n      limit: params.limit,\n    });\n\n    return {\n      content: [{ type: \"text\", text: JSON.stringify(result, null, 2) }],\n    };\n  } catch (e) {\n    return {\n      content: [{ type: \"text\", text: `memory_tunnels error: ${String(e)}` }],\n      isError: true,\n    };\n  }\n}\n","/**\n * PAI Knowledge OS — MCP tool handlers (barrel re-export)\n *\n * All tool implementations have been split into domain modules under\n * src/mcp/tools/. This file re-exports everything so existing imports\n * (from \"../mcp/tools.js\") continue to work unchanged.\n *\n * Domain modules:\n *   tools/types.ts         — shared types + project-row helpers\n *   tools/memory.ts        — memory_search, memory_get\n *   tools/projects.ts      — project_info, project_list, project_detect,\n *                            project_health, project_todo\n *   tools/sessions.ts      — session_list, session_route\n *   tools/registry.ts      — registry_search\n *   tools/notifications.ts — notification_config\n *   tools/topics.ts        — topic_detect\n *   tools/zettel.ts        — zettel_explore, zettel_health, zettel_surprise,\n *                            zettel_suggest, zettel_converse, zettel_themes,\n *                            zettel_god_notes, zettel_communities\n *   tools/observations.ts  — observation_search, observation_timeline\n */\n\nexport * from 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package/dist/{trace-CRx9lPuc.mjs → trace-C2XrzssW.mjs}

@@ -134,4 +134,4 @@ async function handleGraphTrace(backend, params) {
 
 //#endregion
 export { handleGraphTrace };
-//# sourceMappingURL=trace-CRx9lPuc.mjs.map
+//# sourceMappingURL=trace-C2XrzssW.mjs.map

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

@@ -1 +1 @@
-{"version":3,"file":"trace-CRx9lPuc.mjs","names":[],"sources":["../src/graph/trace.ts"],"sourcesContent":["/**\n * trace.ts — graph_trace endpoint handler\n *\n * Given a topic/keyword query, searches vault notes for appearances of that topic\n * and returns a chronological timeline showing how the idea evolved over time.\n */\n\nimport type { StorageBackend } from \"../storage/interface.js\";\n\n// ---------------------------------------------------------------------------\n// Public param / result types\n// ---------------------------------------------------------------------------\n\nexport interface GraphTraceParams {\n  query: string;\n  project_id: number;\n  max_results?: number;\n  lookback_days?: number;\n}\n\nexport interface TraceEntry {\n  vault_path: string;\n  title: string;\n  folder: string;\n  indexed_at: number;\n  snippet: string;\n  dominant_type: string;\n}\n\nexport interface TraceConnection {\n  from_path: string;\n  to_path: string;\n  type: \"temporal\" | \"wikilink\";\n}\n\nexport interface GraphTraceResult {\n  query: string;\n  entries: TraceEntry[];\n  connections: TraceConnection[];\n  time_span: { from: number; to: number };\n}\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\nfunction folderFromPath(vaultPath: string): string {\n  const lastSlash = vaultPath.lastIndexOf(\"/\");\n  return lastSlash === -1 ? \"\" : vaultPath.slice(0, lastSlash);\n}\n\nfunction extractSnippet(text: string, query: string): string {\n  const lowerText = text.toLowerCase();\n  const lowerQuery = query.toLowerCase();\n  const idx = lowerText.indexOf(lowerQuery);\n  if (idx === -1) {\n    return text.slice(0, 160).trimEnd() + (text.length > 160 ? \"…\" : \"\");\n  }\n\n  const CONTEXT = 70;\n  const start = Math.max(0, idx - CONTEXT);\n  const end = Math.min(text.length, idx + query.length + CONTEXT);\n\n  let snippet = text.slice(start, end).replace(/\\s+/g, \" \").trim();\n  if (start > 0) snippet = \"…\" + snippet;\n  if (end < text.length) snippet = snippet + \"…\";\n\n  return snippet;\n}\n\n// ---------------------------------------------------------------------------\n// Main handler\n// ---------------------------------------------------------------------------\n\nexport async function handleGraphTrace(\n  backend: StorageBackend,\n  params: GraphTraceParams\n): Promise<GraphTraceResult> {\n  const query = (params.query ?? 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\"\" : vaultPath.slice(0, lastSlash);\n}\n\nfunction extractSnippet(text: string, query: string): string {\n  const lowerText = text.toLowerCase();\n  const lowerQuery = query.toLowerCase();\n  const idx = lowerText.indexOf(lowerQuery);\n  if (idx === -1) {\n    return text.slice(0, 160).trimEnd() + (text.length > 160 ? \"…\" : \"\");\n  }\n\n  const CONTEXT = 70;\n  const start = Math.max(0, idx - CONTEXT);\n  const end = Math.min(text.length, idx + query.length + CONTEXT);\n\n  let snippet = text.slice(start, end).replace(/\\s+/g, \" \").trim();\n  if (start > 0) snippet = \"…\" + snippet;\n  if (end < text.length) snippet = snippet + \"…\";\n\n  return snippet;\n}\n\n// ---------------------------------------------------------------------------\n// Main handler\n// ---------------------------------------------------------------------------\n\nexport async function handleGraphTrace(\n  backend: StorageBackend,\n  params: GraphTraceParams\n): Promise<GraphTraceResult> {\n  const query = (params.query ?? 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package/dist/{vault-indexer-B-aJpRZC.mjs → vault-indexer-TTCl1QOL.mjs}

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

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

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

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