remem-mcp 0.5.17

package/dist/chunk-34TEZ5U4.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/embedding/local.ts","../src/sdk.ts","../src/security/redactor.ts","../src/storage/sqlite.ts","../src/utils/rrf.ts","../src/wiki/engine.ts"],"sourcesContent":["import { pipeline } from \"@huggingface/transformers\";\nimport type { Embedder } from \"./types.js\";\n\n/**\n * Local embedder. Uses the ONNX runtime and the model all-MiniLM-L6-v2.\n * The vector has 384 dimensions. No API key is needed.\n *\n * The first run downloads the model. Subsequent runs load the model from the disk cache.\n */\nexport class LocalEmbedder implements Embedder {\n  readonly dimension = 384;\n  readonly model = \"Xenova/all-MiniLM-L6-v2\";\n\n  private extractor: Awaited<ReturnType<typeof pipeline>> | null = null;\n  private initPromise: Promise<void> | null = null;\n\n  /** Initialize the model. This runs once. Subsequent calls return immediately. */\n  private async init(): Promise<void> {\n    if (this.extractor) return;\n    if (this.initPromise) {\n      await this.initPromise;\n      return;\n    }\n    this.initPromise = (async () => {\n      this.extractor = await pipeline(\"feature-extraction\", this.model);\n    })();\n    await this.initPromise;\n  }\n\n  async embed(text: string): Promise<number[]> {\n    await this.init();\n    if (!this.extractor) throw new Error(\"Embedder failed to initialize\");\n\n    const output = await this.extractor(text, { pooling: \"mean\", normalize: true });\n    // output.data is a Float32Array\n    return Array.from(output.data as Float32Array);\n  }\n}\n","/**\n * Programmatic API for remem-mcp.\n * Use this to embed memory directly in your application without MCP.\n *\n * @example\n * ```ts\n * import { Memory } from \"remem-mcp\";\n *\n * const memory = new Memory();\n * await memory.capture(\"We chose SQLite for storage.\", \"decision\", [\"arch\"]);\n * const results = await memory.recall(\"storage decision\");\n * ```\n */\n\nimport { createHash } from \"node:crypto\";\nimport { homedir } from \"node:os\";\nimport { join } from \"node:path\";\nimport { LocalEmbedder } from \"./embedding/local.js\";\nimport { redact } from \"./security/redactor.js\";\nimport { SQLiteBackend } from \"./storage/sqlite.js\";\nimport type {\n  CaptureEntry,\n  CaptureType,\n  DeleteFilter,\n  DeleteResult,\n  SearchFilters,\n  SearchMode,\n  SearchResult,\n} from \"./storage/types.js\";\nimport { generateId } from \"./utils/ulid.js\";\n\nexport type {\n  CaptureEntry,\n  CaptureType,\n  DeleteFilter,\n  DeleteResult,\n  SearchFilters,\n  SearchMode,\n  SearchResult,\n};\nexport { LocalEmbedder, SQLiteBackend };\n\n/** High-level memory API. */\nexport class Memory {\n  private storage: SQLiteBackend;\n  private embedder: LocalEmbedder;\n  private sessionKey: string;\n  private redactSecrets: boolean;\n\n  constructor(opts?: {\n    dbPath?: string;\n    sessionKey?: string;\n    redactSecrets?: boolean;\n  }) {\n    const dbPath =\n      opts?.dbPath ?? join(homedir(), \".local\", \"share\", \"remem-mcp\", \"memory.db\");\n    this.storage = new SQLiteBackend(dbPath);\n    this.embedder = new LocalEmbedder();\n    this.sessionKey =\n      opts?.sessionKey ??\n      process.env.TDAI_SESSION_KEY ??\n      createHash(\"sha256\").update(process.cwd()).digest(\"hex\").slice(0, 16);\n    this.redactSecrets = opts?.redactSecrets ?? true;\n  }\n\n  /** Capture a memory entry. Returns the ID, or null if duplicate. */\n  async capture(content: string, type: CaptureType, tags: string[] = []): Promise<string | null> {\n    const { text: redactedContent } = this.redactSecrets ? redact(content) : { text: content };\n\n    // Dedup check\n    const contentHash = createHash(\"sha256\").update(redactedContent).digest(\"hex\");\n    const existing = await this.storage.findByContentHash(contentHash, this.sessionKey);\n    if (existing.length > 0) return null;\n\n    const id = generateId();\n    const entry: CaptureEntry = {\n      id,\n      sessionKey: this.sessionKey,\n      agentId: \"sdk\",\n      type,\n      content: redactedContent,\n      tags,\n      createdAt: Date.now(),\n    };\n\n    await this.storage.put(entry);\n\n    try {\n      const embedding = await this.embedder.embed(redactedContent);\n      await this.storage.putVector(id, embedding);\n    } catch {\n      // Embedding is optional\n    }\n\n    return id;\n  }\n\n  /** Recall relevant memory. */\n  async recall(\n    query: string,\n    opts?: { limit?: number; mode?: SearchMode },\n  ): Promise<SearchResult[]> {\n    const limit = Math.min(opts?.limit ?? 10, 50);\n    const mode = opts?.mode ?? \"hybrid\";\n\n    let queryEmbedding: number[] | null = null;\n    if (mode === \"hybrid\" || mode === \"vector\") {\n      queryEmbedding = await this.embedder.embed(query);\n    }\n\n    return this.storage.search(query, queryEmbedding, {\n      sessionKey: this.sessionKey,\n      limit,\n      offset: 0,\n      mode,\n    });\n  }\n\n  /** Search with filters. */\n  async search(\n    query: string,\n    opts?: { mode?: SearchMode; filters?: SearchFilters; limit?: number },\n  ): Promise<SearchResult[]> {\n    const limit = Math.min(opts?.limit ?? 20, 100);\n    const mode = opts?.mode ?? \"hybrid\";\n\n    let queryEmbedding: number[] | null = null;\n    if (mode === \"hybrid\" || mode === \"vector\") {\n      queryEmbedding = await this.embedder.embed(query);\n    }\n\n    return this.storage.search(query, queryEmbedding, {\n      limit,\n      offset: 0,\n      mode,\n      filters: opts?.filters,\n    });\n  }\n\n  /** Delete a capture by ID. */\n  async forget(id: string): Promise<DeleteResult> {\n    return this.storage.delete(id);\n  }\n\n  /** Create a handoff packet for the next agent session. */\n  async handoff(opts: {\n    task: string;\n    status: \"in_progress\" | \"blocked\" | \"needs_review\" | \"done\" | \"assigned\";\n    progress: string;\n    decisions?: string[];\n    files?: string[];\n    nextSteps?: string[];\n  }): Promise<string | null> {\n    const lines: string[] = [];\n    lines.push(`# Handoff: ${opts.task}`);\n    lines.push(`Status: ${opts.status}`);\n    lines.push(`Date: ${new Date().toISOString()}`);\n    lines.push(\"\");\n    lines.push(\"## Progress\");\n    lines.push(opts.progress);\n    lines.push(\"\");\n\n    if (opts.decisions && opts.decisions.length > 0) {\n      lines.push(\"## Decisions\");\n      for (const d of opts.decisions) lines.push(`- ${d}`);\n      lines.push(\"\");\n    }\n    if (opts.files && opts.files.length > 0) {\n      lines.push(\"## Files\");\n      for (const f of opts.files) lines.push(`- ${f}`);\n      lines.push(\"\");\n    }\n    if (opts.nextSteps && opts.nextSteps.length > 0) {\n      lines.push(\"## Next steps\");\n      opts.nextSteps.forEach((s, i) => {\n        lines.push(`${i + 1}. ${s}`);\n      });\n      lines.push(\"\");\n    }\n\n    const content = lines.join(\"\\n\");\n    // Dedup: hash the structured data (excluding the timestamp)\n    const dedupPayload = JSON.stringify({\n      task: opts.task,\n      status: opts.status,\n      progress: opts.progress,\n      decisions: opts.decisions ?? [],\n      files: opts.files ?? [],\n      nextSteps: opts.nextSteps ?? [],\n    });\n    const contentHash = createHash(\"sha256\").update(dedupPayload).digest(\"hex\");\n    const existing = await this.storage.findByContentHash(contentHash, this.sessionKey);\n    if (existing.length > 0) return null;\n\n    const id = generateId();\n    const entry: CaptureEntry = {\n      id,\n      sessionKey: this.sessionKey,\n      agentId: \"sdk\",\n      type: \"task\",\n      content,\n      tags: [\"handoff\", `status:${opts.status}`],\n      createdAt: Date.now(),\n      metadata: {\n        handoff: true,\n        task: opts.task,\n        status: opts.status,\n        progress: opts.progress,\n        decisions: opts.decisions ?? [],\n        files: opts.files ?? [],\n        nextSteps: opts.nextSteps ?? [],\n      },\n      contentHash,\n    };\n\n    await this.storage.put(entry);\n\n    try {\n      const embedding = await this.embedder.embed(content);\n      await this.storage.putVector(id, embedding);\n    } catch {\n      // Embedding is optional\n    }\n\n    return id;\n  }\n\n  /** Record an Architecture Decision Record (ADR). */\n  async adr(opts: {\n    title: string;\n    context: string;\n    decision: string;\n    alternatives?: string[];\n    consequences?: string;\n    tags?: string[];\n  }): Promise<string | null> {\n    const lines: string[] = [];\n    lines.push(`# ADR: ${opts.title}`);\n    lines.push(`Date: ${new Date().toISOString()}`);\n    lines.push(\"\");\n    lines.push(\"## Context\");\n    lines.push(opts.context);\n    lines.push(\"\");\n    lines.push(\"## Decision\");\n    lines.push(opts.decision);\n    lines.push(\"\");\n\n    const alternatives = Array.isArray(opts.alternatives)\n      ? opts.alternatives\n      : typeof opts.alternatives === \"string\" && opts.alternatives\n        ? [opts.alternatives]\n        : [];\n    if (alternatives.length > 0) {\n      lines.push(\"## Alternatives considered\");\n      for (const alt of alternatives) lines.push(`- ${alt}`);\n      lines.push(\"\");\n    }\n    if (opts.consequences) {\n      lines.push(\"## Consequences\");\n      lines.push(opts.consequences);\n      lines.push(\"\");\n    }\n\n    const content = lines.join(\"\\n\");\n    const dedupPayload = JSON.stringify({\n      title: opts.title,\n      context: opts.context,\n      decision: opts.decision,\n      alternatives,\n      consequences: opts.consequences ?? \"\",\n    });\n    const contentHash = createHash(\"sha256\").update(dedupPayload).digest(\"hex\");\n    const existing = await this.storage.findByContentHash(contentHash, this.sessionKey);\n    if (existing.length > 0) return null;\n\n    const id = generateId();\n    const entry: CaptureEntry = {\n      id,\n      sessionKey: this.sessionKey,\n      agentId: \"sdk\",\n      type: \"decision\",\n      content,\n      tags: [\"adr\", ...(opts.tags ?? [])],\n      createdAt: Date.now(),\n      metadata: {\n        adr: true,\n        title: opts.title,\n        context: opts.context,\n        decision: opts.decision,\n        alternatives,\n        consequences: opts.consequences ?? \"\",\n      },\n      contentHash,\n    };\n\n    await this.storage.put(entry);\n\n    try {\n      const embedding = await this.embedder.embed(content);\n      await this.storage.putVector(id, embedding);\n    } catch {\n      // Embedding is optional\n    }\n\n    return id;\n  }\n\n  /** Close the database connection. */\n  close(): void {\n    this.storage.close();\n  }\n}\n\nexport type {\n  CallInfo,\n  ImpactResult,\n  ImportInfo,\n  IndexResult,\n  SymbolInfo,\n} from \"./codegraph/engine.js\";\n// Re-export CodeGraph engine for programmatic use\nexport {\n  detectLanguage,\n  findCallees,\n  findCallers,\n  impactAnalysis,\n  indexDirectory,\n  indexFile,\n  listSymbols,\n  SUPPORTED_LANGUAGES,\n  searchSymbols,\n} from \"./codegraph/engine.js\";\nexport type { IngestResult as WikiIngestResult, WikiLink, WikiPage } from \"./wiki/engine.js\";\n// Re-export Wiki engine for programmatic use\nexport {\n  findOutdatedPages,\n  getWikiPage,\n  ingestDirectory as wikiIngestDirectory,\n  ingestFile as wikiIngestFile,\n  searchWiki,\n} from \"./wiki/engine.js\";\n","/**\n * Secret redactor.\n * Scans text for secrets and replaces them with [REDACTED].\n * Uses regex patterns and a high-entropy detector.\n */\n\n/** Regex patterns for known secret formats. */\nconst SECRET_PATTERNS: RegExp[] = [\n  // OpenAI API key\n  /sk-[a-zA-Z0-9]{20,}/g,\n  // Anthropic API key\n  /sk-ant-[a-zA-Z0-9-]+/g,\n  // GitHub personal access token\n  /ghp_[a-zA-Z0-9]{36}/g,\n  // GitHub OAuth token\n  /gho_[a-zA-Z0-9]{36}/g,\n  // GitHub fine-grained token\n  /github_pat_[a-zA-Z0-9_]{82}/g,\n  // Slack token\n  /xox[baprs]-[a-zA-Z0-9-]+/g,\n  // AWS access key ID\n  /AKIA[0-9A-Z]{16}/g,\n  // AWS secret access key (40 chars, base64-ish)\n  /(?<![A-Za-z0-9+/])[A-Za-z0-9+/]{40}(?![A-Za-z0-9+/])/g,\n  // PEM private key block\n  /-----BEGIN [A-Z ]*PRIVATE KEY-----[\\s\\S]*?-----END [A-Z ]*PRIVATE KEY-----/g,\n  // Google API key\n  /AIza[0-9A-Za-z\\-_]{35}/g,\n  // Generic bearer token (require 20+ char token to avoid redacting \"Bearer with JWT\")\n  /Bearer\\s+[a-zA-Z0-9\\-._~+/]{20,}=*/g,\n];\n\n/** Minimum length for high-entropy detection. */\nconst MIN_LENGTH = 40;\n\n/** Entropy threshold in bits per character. */\nconst ENTROPY_THRESHOLD = 4.5;\n\n/** Compute the Shannon entropy of a string, in bits per character. */\nfunction shannonEntropy(str: string): number {\n  const freq = new Map<string, number>();\n  for (const ch of str) {\n    freq.set(ch, (freq.get(ch) ?? 0) + 1);\n  }\n  let entropy = 0;\n  const len = str.length;\n  for (const count of freq.values()) {\n    const p = count / len;\n    entropy -= p * Math.log2(p);\n  }\n  return entropy;\n}\n\n/** Find high-entropy strings that look like secrets. */\nfunction findHighEntropyStrings(text: string): string[] {\n  const results: string[] = [];\n  // Match long strings of alphanumeric, +, /, =\n  const regex = /[a-zA-Z0-9+/=]{40,}/g;\n  let match: RegExpExecArray | null;\n  match = regex.exec(text);\n  while (match !== null) {\n    const str = match[0];\n    if (str.length >= MIN_LENGTH) {\n      const entropy = shannonEntropy(str);\n      if (entropy >= ENTROPY_THRESHOLD) {\n        results.push(str);\n      }\n    }\n    match = regex.exec(text);\n  }\n  return results;\n}\n\nexport interface RedactionResult {\n  /** The redacted text. */\n  text: string;\n  /** Whether any secrets were found and redacted. */\n  redacted: boolean;\n}\n\n/** Redact secrets from text. Returns the redacted text and a flag. */\nexport function redact(text: string): RedactionResult {\n  let result = text;\n  let redacted = false;\n\n  // Apply regex patterns\n  for (const pattern of SECRET_PATTERNS) {\n    const before = result;\n    result = result.replace(pattern, \"[REDACTED]\");\n    if (result !== before) redacted = true;\n  }\n\n  // Apply high-entropy detection\n  const highEntropy = findHighEntropyStrings(result);\n  for (const str of highEntropy) {\n    // Make sure we did not already redact this region\n    result = result.replace(str, \"[REDACTED]\");\n    redacted = true;\n  }\n\n  return { text: result, redacted };\n}\n","import { createHash } from \"node:crypto\";\nimport { copyFileSync, existsSync, mkdirSync, readFileSync } from \"node:fs\";\nimport { dirname, join } from \"node:path\";\nimport { fileURLToPath } from \"node:url\";\nimport Database from \"better-sqlite3\";\nimport * as sqliteVec from \"sqlite-vec\";\nimport { type RankedResult, rrfMerge } from \"../utils/rrf.js\";\nimport { generateId } from \"../utils/ulid.js\";\nimport type {\n  AtomEntry,\n  CaptureEntry,\n  ConflictResult,\n  DeleteFilter,\n  DeleteResult,\n  KnowledgeEntry,\n  MessageRow,\n  PersonaEntry,\n  QueryOptions,\n  ResolveResult,\n  ScenarioEntry,\n  SearchResult,\n  SkillEntry,\n  StorageBackend,\n  TrustState,\n} from \"./types.js\";\n\nconst __dirname = dirname(fileURLToPath(import.meta.url));\n\n/** Current schema version. */\nconst CURRENT_SCHEMA_VERSION = 6;\n\n/**\n * SQLite storage backend.\n * Uses better-sqlite3 + sqlite-vec + FTS5.\n * Default backend. Zero setup.\n */\nexport class SQLiteBackend implements StorageBackend {\n  private db: Database.Database;\n\n  /** Get the underlying database instance (for CodeGraph/Wiki operations). */\n  getDatabase(): Database.Database {\n    return this.db;\n  }\n\n  constructor(dbPath: string) {\n    // Make sure the directory exists\n    const dir = dirname(dbPath);\n    if (!existsSync(dir)) mkdirSync(dir, { recursive: true });\n\n    // Try read-write first; fall back to read-only if the directory is not writable\n    // (e.g. Codex CLI sandbox blocks writes outside the workdir)\n    let readonly = false;\n    try {\n      this.db = new Database(dbPath);\n      this.db.pragma(\"journal_mode = WAL\");\n    } catch {\n      // Read-only fallback — recall/search still work, captures will fail gracefully\n      readonly = true;\n      this.db = new Database(dbPath, { readonly: true });\n    }\n\n    // Pragmas that are safe for both read-write and read-only\n    try {\n      this.db.pragma(\"busy_timeout = 5000\");\n    } catch {\n      /* read-only */\n    }\n    if (!readonly) {\n      this.db.pragma(\"synchronous = NORMAL\");\n      this.db.pragma(\"foreign_keys = OFF\");\n    }\n\n    // Load the sqlite-vec extension\n    sqliteVec.load(this.db);\n\n    // Detect the database state and run the migration (skipped in read-only mode)\n    if (!readonly) {\n      try {\n        this.detectAndMigrate(dbPath);\n      } catch {\n        // Migration failed — non-fatal, schema might already be correct\n      }\n    }\n  }\n\n  /**\n   * Detect the database state and run the correct migration path.\n   */\n  private detectAndMigrate(dbPath: string): void {\n    const hasVersionTable = this.db\n      .prepare(\"SELECT name FROM sqlite_master WHERE type='table' AND name='schema_version'\")\n      .get() as { name: string } | undefined;\n\n    if (!hasVersionTable) {\n      // Fresh database or old database without versioning\n      const tables = this.db\n        .prepare(\"SELECT name FROM sqlite_master WHERE type='table' AND name NOT LIKE 'sqlite_%'\")\n        .all() as { name: string }[];\n\n      if (tables.length === 0) {\n        // Fresh database: run the full schema, write current version\n        this.runSchema();\n        this.writeSchemaVersion(CURRENT_SCHEMA_VERSION);\n      } else {\n        // Old database without versioning. Backup, then run incremental migrations\n        // to add missing columns before running the full schema (which creates new tables).\n        this.backupDatabase(dbPath);\n        this.migrateV1ToV2();\n        this.migrateV2ToV3();\n        this.migrateV3ToV4();\n        this.migrateV4ToV5();\n        this.migrateV5ToV6();\n        // Now run the full schema to create any remaining tables/triggers/indexes\n        this.runSchema();\n        this.writeSchemaVersion(CURRENT_SCHEMA_VERSION);\n      }\n      return;\n    }\n\n    // Database has a schema_version table. Read the current version.\n    const row = this.db.prepare(\"SELECT MAX(version) as version FROM schema_version\").get() as\n      | { version: number }\n      | undefined;\n    const currentVersion = row?.version ?? 0;\n\n    if (currentVersion < 1) {\n      this.backupDatabase(dbPath);\n      this.runSchema();\n      this.writeSchemaVersion(1);\n    }\n    if (currentVersion < 2) {\n      this.backupDatabase(dbPath);\n      this.migrateV1ToV2();\n      this.writeSchemaVersion(2);\n    }\n    if (currentVersion < 3) {\n      this.backupDatabase(dbPath);\n      this.migrateV2ToV3();\n      this.writeSchemaVersion(3);\n    }\n    if (currentVersion < 4) {\n      this.backupDatabase(dbPath);\n      this.migrateV3ToV4();\n      this.writeSchemaVersion(4);\n    }\n    if (currentVersion < 5) {\n      this.backupDatabase(dbPath);\n      this.migrateV4ToV5();\n      this.writeSchemaVersion(5);\n    }\n    if (currentVersion < 6) {\n      // Tables are created by runSchema() via CREATE TABLE IF NOT EXISTS.\n      // Run schema to create CodeGraph + Wiki tables.\n      this.runSchema();\n      this.migrateV5ToV6();\n      this.writeSchemaVersion(6);\n    }\n  }\n\n  /** Backup the database to a .bak file. */\n  private backupDatabase(dbPath: string): void {\n    const backupPath = `${dbPath}.bak`;\n    try {\n      this.db.pragma(\"wal_checkpoint(FULL)\");\n      copyFileSync(dbPath, backupPath);\n      console.error(`[remem-mcp] Backed up database to ${backupPath}`);\n    } catch (err) {\n      console.error(`[remem-mcp] Backup failed: ${err}`);\n    }\n  }\n\n  /** Run the schema.sql file. Idempotent. */\n  private runSchema(): void {\n    const candidates = [\n      join(__dirname, \"storage\", \"schema.sql\"),\n      join(__dirname, \"schema.sql\"),\n      join(__dirname, \"..\", \"storage\", \"schema.sql\"),\n    ];\n\n    let schema: string | null = null;\n    for (const path of candidates) {\n      try {\n        schema = readFileSync(path, \"utf-8\");\n        break;\n      } catch {\n        // Try the next candidate\n      }\n    }\n\n    if (!schema) {\n      throw new Error(\"Could not find schema.sql. Make sure the build copied it to dist/storage/.\");\n    }\n    this.db.exec(schema);\n  }\n\n  /** Write the schema version to the schema_version table. */\n  private writeSchemaVersion(version: number): void {\n    this.db\n      .prepare(\"INSERT INTO schema_version (version, applied_at) VALUES (?, ?)\")\n      .run(version, Date.now());\n  }\n\n  /** Migrate schema v1 → v2: add content_hash column + index. */\n  private migrateV1ToV2(): void {\n    const cols = this.db.prepare(\"PRAGMA table_info(captures)\").all() as { name: string }[];\n    const hasContentHash = cols.some((c) => c.name === \"content_hash\");\n    if (!hasContentHash) {\n      this.db.exec(\"ALTER TABLE captures ADD COLUMN content_hash TEXT\");\n      console.error(\"[remem-mcp] Added content_hash column to captures\");\n    }\n    const idxs = this.db\n      .prepare(\"SELECT name FROM sqlite_master WHERE type='index' AND name='idx_captures_hash'\")\n      .get() as { name: string } | undefined;\n    if (!idxs) {\n      this.db.exec(\"CREATE INDEX IF NOT EXISTS idx_captures_hash ON captures (content_hash)\");\n    }\n    // Backfill content_hash for existing rows\n    const rows = this.db\n      .prepare(\"SELECT id, content FROM captures WHERE content_hash IS NULL\")\n      .all() as { id: string; content: string }[];\n    const stmt = this.db.prepare(\"UPDATE captures SET content_hash = ? WHERE id = ?\");\n    for (const row of rows) {\n      const hash = createHash(\"sha256\").update(row.content).digest(\"hex\");\n      stmt.run(hash, row.id);\n    }\n    if (rows.length > 0) {\n      console.error(`[remem-mcp] Backfilled content_hash for ${rows.length} existing captures`);\n    }\n  }\n\n  /** Migrate schema v2 → v3: add multi-tenant columns + new tables (messages, knowledge, skills, persona). */\n  private migrateV2ToV3(): void {\n    // Helper: add a column to a table if the table exists and the column is missing\n    const addColumnIfMissing = (table: string, column: string, definition: string) => {\n      const tableExists = this.db\n        .prepare(\"SELECT name FROM sqlite_master WHERE type='table' AND name=?\")\n        .get(table) as { name: string } | undefined;\n      if (!tableExists) return;\n      const cols = this.db.prepare(`PRAGMA table_info(${table})`).all() as { name: string }[];\n      if (!cols.some((c) => c.name === column)) {\n        this.db.exec(`ALTER TABLE ${table} ADD COLUMN ${column} ${definition}`);\n      }\n    };\n\n    // Add multi-tenant columns to captures\n    addColumnIfMissing(\"captures\", \"team_id\", \"TEXT\");\n    addColumnIfMissing(\"captures\", \"user_id\", \"TEXT\");\n    addColumnIfMissing(\"captures\", \"task_id\", \"TEXT\");\n\n    // Add multi-tenant columns to atoms\n    addColumnIfMissing(\"atoms\", \"team_id\", \"TEXT\");\n    addColumnIfMissing(\"atoms\", \"agent_id\", \"TEXT\");\n    addColumnIfMissing(\"atoms\", \"user_id\", \"TEXT\");\n\n    // Add multi-tenant columns to scenarios\n    addColumnIfMissing(\"scenarios\", \"team_id\", \"TEXT\");\n    addColumnIfMissing(\"scenarios\", \"agent_id\", \"TEXT\");\n    addColumnIfMissing(\"scenarios\", \"user_id\", \"TEXT\");\n\n    // Create new tables (idempotent — schema.sql also has them, but run here for migration path\n    // before schema.sql so that index creation in schema.sql doesn't fail)\n    this.db.exec(`\n      CREATE TABLE IF NOT EXISTS messages (\n        id          TEXT PRIMARY KEY,\n        capture_id  TEXT NOT NULL REFERENCES captures(id) ON DELETE CASCADE,\n        role        TEXT NOT NULL,\n        content     TEXT NOT NULL,\n        seq         INTEGER NOT NULL,\n        created_at  INTEGER NOT NULL\n      );\n      CREATE TABLE IF NOT EXISTS persona (\n        team_id    TEXT NOT NULL,\n        agent_id   TEXT NOT NULL,\n        user_id    TEXT NOT NULL,\n        content    TEXT NOT NULL,\n        updated_at INTEGER NOT NULL,\n        PRIMARY KEY (team_id, agent_id, user_id)\n      );\n      CREATE TABLE IF NOT EXISTS knowledge (\n        id          TEXT PRIMARY KEY,\n        team_id     TEXT NOT NULL,\n        name        TEXT NOT NULL,\n        type        TEXT NOT NULL,\n        summary     TEXT,\n        service_url TEXT,\n        repo_url    TEXT,\n        branch      TEXT,\n        created_at  INTEGER NOT NULL\n      );\n      CREATE TABLE IF NOT EXISTS skills (\n        id          TEXT PRIMARY KEY,\n        team_id     TEXT NOT NULL,\n        agent_id    TEXT,\n        name        TEXT NOT NULL,\n        description TEXT,\n        content     TEXT,\n        version     INTEGER NOT NULL DEFAULT 1,\n        created_at  INTEGER NOT NULL,\n        updated_at  INTEGER NOT NULL\n      );\n    `);\n    // Indexes are created by the full schema.sql run, not here.\n\n    console.error(\n      \"[remem-mcp] Migrated schema v2 → v3 (multi-tenant + messages + knowledge + skills + persona)\",\n    );\n  }\n\n  /** Migrate schema v3 → v4: add deleted_at column for soft delete (tombstone). */\n  private migrateV3ToV4(): void {\n    const cols = this.db.prepare(\"PRAGMA table_info(captures)\").all() as { name: string }[];\n    const hasDeletedAt = cols.some((c) => c.name === \"deleted_at\");\n    if (!hasDeletedAt) {\n      this.db.exec(\"ALTER TABLE captures ADD COLUMN deleted_at INTEGER\");\n      console.error(\"[remem-mcp] Added deleted_at column to captures (tombstone support)\");\n    }\n    console.error(\"[remem-mcp] Migrated schema v3 → v4 (tombstone / soft delete)\");\n  }\n\n  /** Migrate schema v4 → v5: add trust_state, rejection_reason, superseded_by columns. */\n  private migrateV4ToV5(): void {\n    const cols = this.db.prepare(\"PRAGMA table_info(captures)\").all() as { name: string }[];\n    const hasTrustState = cols.some((c) => c.name === \"trust_state\");\n    if (!hasTrustState) {\n      this.db.exec(\"ALTER TABLE captures ADD COLUMN trust_state TEXT NOT NULL DEFAULT 'candidate'\");\n      console.error(\"[remem-mcp] Added trust_state column to captures\");\n    }\n    const hasRejectionReason = cols.some((c) => c.name === \"rejection_reason\");\n    if (!hasRejectionReason) {\n      this.db.exec(\"ALTER TABLE captures ADD COLUMN rejection_reason TEXT\");\n      console.error(\"[remem-mcp] Added rejection_reason column to captures\");\n    }\n    const hasSupersededBy = cols.some((c) => c.name === \"superseded_by\");\n    if (!hasSupersededBy) {\n      this.db.exec(\"ALTER TABLE captures ADD COLUMN superseded_by TEXT REFERENCES captures(id)\");\n      console.error(\"[remem-mcp] Added superseded_by column to captures\");\n    }\n    this.db.exec(\"CREATE INDEX IF NOT EXISTS idx_captures_trust ON captures (trust_state)\");\n    this.db.exec(\n      \"CREATE INDEX IF NOT EXISTS idx_captures_rejected_hash ON captures (content_hash) WHERE trust_state = 'rejected'\",\n    );\n    console.error(\"[remem-mcp] Migrated schema v4 → v5 (trust state + correction)\");\n  }\n\n  /** Migrate schema v5 → v6: add CodeGraph + Wiki tables (created by runSchema). */\n  private migrateV5ToV6(): void {\n    // Tables are created by runSchema() which runs CREATE TABLE IF NOT EXISTS.\n    // This migration is a no-op placeholder for version tracking.\n    console.error(\"[remem-mcp] Migrated schema v5 → v6 (CodeGraph + Wiki tables)\");\n  }\n\n  async put(entry: CaptureEntry): Promise<void> {\n    const contentHash =\n      entry.contentHash ?? createHash(\"sha256\").update(entry.content).digest(\"hex\");\n    const stmt = this.db.prepare(`\n      INSERT INTO captures (id, session_key, agent_id, type, content, content_hash, tags, created_at, metadata, team_id, user_id, task_id, trust_state)\n      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n    `);\n    stmt.run(\n      entry.id,\n      entry.sessionKey,\n      entry.agentId,\n      entry.type,\n      entry.content,\n      contentHash,\n      JSON.stringify(entry.tags),\n      entry.createdAt,\n      entry.metadata ? JSON.stringify(entry.metadata) : null,\n      entry.teamId ?? null,\n      entry.userId ?? null,\n      entry.taskId ?? null,\n      entry.trustState ?? \"candidate\",\n    );\n\n    // Store role-based messages if provided\n    if (entry.messages && entry.messages.length > 0) {\n      const msgStmt = this.db.prepare(\n        \"INSERT INTO messages (id, capture_id, role, content, seq, created_at) VALUES (?, ?, ?, ?, ?, ?)\",\n      );\n      for (let i = 0; i < entry.messages.length; i++) {\n        const msg = entry.messages[i];\n        msgStmt.run(generateId(), entry.id, msg.role, msg.content, i, entry.createdAt);\n      }\n    }\n  }\n\n  async putVector(id: string, embedding: number[]): Promise<void> {\n    const buffer = new Float32Array(embedding);\n    const stmt = this.db.prepare(\"INSERT INTO captures_vec (id, embedding) VALUES (?, ?)\");\n    stmt.run(id, Buffer.from(buffer.buffer));\n  }\n\n  async get(id: string): Promise<CaptureEntry | null> {\n    const row = this.db\n      .prepare(\"SELECT * FROM captures WHERE id = ? AND deleted_at IS NULL\")\n      .get(id) as DbRow | undefined;\n    if (!row) return null;\n    return rowToEntry(row);\n  }\n\n  async findRejectedByContentHash(\n    contentHash: string,\n    sessionKey?: string,\n  ): Promise<CaptureEntry[]> {\n    let sql = \"SELECT * FROM captures WHERE content_hash = ? AND trust_state = 'rejected'\";\n    const params: unknown[] = [contentHash];\n    if (sessionKey) {\n      sql += \" AND session_key = ?\";\n      params.push(sessionKey);\n    }\n    const rows = this.db.prepare(sql).all(...params) as DbRow[];\n    return rows.map(rowToEntry);\n  }\n\n  async getMessages(captureId: string): Promise<MessageRow[]> {\n    const rows = this.db\n      .prepare(\"SELECT * FROM messages WHERE capture_id = ? ORDER BY seq ASC\")\n      .all(captureId) as MessageDbRow[];\n    return rows.map((r) => ({\n      id: r.id,\n      captureId: r.capture_id,\n      role: r.role,\n      content: r.content,\n      seq: r.seq,\n      createdAt: r.created_at,\n    }));\n  }\n\n  async findByContentHash(contentHash: string, sessionKey?: string): Promise<CaptureEntry[]> {\n    let sql = \"SELECT * FROM captures WHERE content_hash = ? AND deleted_at IS NULL\";\n    const params: unknown[] = [contentHash];\n    if (sessionKey) {\n      sql += \" AND session_key = ?\";\n      params.push(sessionKey);\n    }\n    const rows = this.db.prepare(sql).all(...params) as DbRow[];\n    return rows.map(rowToEntry);\n  }\n\n  async listByTags(tags: string[], limit = 50): Promise<CaptureEntry[]> {\n    if (tags.length === 0) return [];\n    const tagConditions = tags.map(() => \"tags LIKE ?\").join(\" OR \");\n    const sql = `SELECT * FROM captures WHERE (${tagConditions}) AND deleted_at IS NULL AND trust_state != 'rejected' ORDER BY created_at DESC LIMIT ?`;\n    const params = [...tags.map((t) => `%\"${t}\"%`), limit];\n    const rows = this.db.prepare(sql).all(...params) as DbRow[];\n    return rows.map(rowToEntry);\n  }\n\n  async search(\n    query: string,\n    queryEmbedding: number[] | null,\n    opts: QueryOptions,\n  ): Promise<SearchResult[]> {\n    const { mode, limit, offset, sessionKey, filters } = opts;\n\n    // Detect temporal intent: queries asking for \"current/latest/now\" state\n    // should strongly prefer recent memories over older ones with better keyword match.\n    const temporalIntent = /\\b(currently|current|now|latest|new|present|today|active)\\b/i.test(query);\n\n    let bm25Results: RankedResult[] = [];\n    let vecResults: RankedResult[] = [];\n\n    // In hybrid mode, use different candidate pool sizes for each channel:\n    // - BM25: tight pool (limit*2) for high precision — only best keyword matches\n    // - Vector: very broad pool (limit*10, cap 1000) for high recall at scale\n    // This ensures seed memories stored among 1000+ distractors are still found.\n    // RRF fusion with weighted vector search filters out BM25 noise.\n    const bm25CandidateLimit = mode === \"hybrid\" ? limit * 2 : limit * 2;\n    const vecCandidateLimit = mode === \"hybrid\" ? Math.min(Math.max(limit * 10, 100), 1000) : limit * 2;\n\n    // BM25 search (FTS5)\n    if (mode === \"hybrid\" || mode === \"keyword\") {\n      bm25Results = this.bm25Search(query, bm25CandidateLimit, sessionKey, filters);\n    }\n\n    // Vector search (sqlite-vec)\n    if ((mode === \"hybrid\" || mode === \"vector\") && queryEmbedding) {\n      vecResults = this.vectorSearch(queryEmbedding, vecCandidateLimit, sessionKey, filters);\n    }\n\n    if (mode === \"keyword\") {\n      return this.fetchEntries(bm25Results, limit, offset, temporalIntent);\n    }\n    if (mode === \"vector\") {\n      return this.fetchEntries(vecResults, limit, offset, temporalIntent);\n    }\n\n    // Hybrid: fuse with RRF\n    const fused = rrfMerge(bm25Results, vecResults, limit + offset);\n    const paged = fused.slice(offset, offset + limit);\n    return this.fetchEntriesById(paged, temporalIntent);\n  }\n\n  /** Run a BM25 search via FTS5. */\n  private bm25Search(\n    query: string,\n    limit: number,\n    sessionKey?: string,\n    filters?: QueryOptions[\"filters\"],\n  ): RankedResult[] {\n    const ftsQuery = this.escapeFtsQuery(query);\n    if (!ftsQuery) return [];\n\n    let sql: string;\n    const params: unknown[] = [ftsQuery];\n    try {\n      sql = `\n      SELECT fts.id as id, bm25(captures_fts) as score\n      FROM captures_fts fts\n      JOIN captures c ON c.id = fts.id\n      WHERE captures_fts MATCH ? AND c.deleted_at IS NULL AND c.trust_state != 'rejected'\n    `;\n\n      if (sessionKey) {\n        sql += \" AND c.session_key = ?\";\n        params.push(sessionKey);\n      }\n      if (filters?.type) {\n        sql += \" AND c.type = ?\";\n        params.push(filters.type);\n      }\n      if (filters?.agentId) {\n        sql += \" AND c.agent_id = ?\";\n        params.push(filters.agentId);\n      }\n      if (filters?.teamId) {\n        sql += \" AND c.team_id = ?\";\n        params.push(filters.teamId);\n      }\n      if (filters?.userId) {\n        sql += \" AND c.user_id = ?\";\n        params.push(filters.userId);\n      }\n      if (filters?.taskId) {\n        sql += \" AND c.task_id = ?\";\n        params.push(filters.taskId);\n      }\n      if (filters?.tags && filters.tags.length > 0) {\n        const tagConditions = filters.tags.map(() => \"c.tags LIKE ?\").join(\" OR \");\n        sql += ` AND (${tagConditions})`;\n        params.push(...filters.tags.map((t) => `%\"${t}\"%`));\n      }\n      if (filters?.dateFrom) {\n        sql += \" AND c.created_at >= ?\";\n        params.push(new Date(filters.dateFrom).getTime());\n      }\n      if (filters?.dateTo) {\n        sql += \" AND c.created_at <= ?\";\n        params.push(new Date(filters.dateTo).getTime());\n      }\n\n      sql += \" ORDER BY score LIMIT ?\";\n      params.push(limit);\n\n      const rows = this.db.prepare(sql).all(...params) as { id: string; score: number }[];\n      return rows.map((r) => ({ id: r.id, score: r.score }));\n    } catch (err: unknown) {\n      // FTS5 external content tables can get out of sync after schema changes\n      // or crashes. Rebuild the index and retry once.\n      if (err instanceof Error && err.message.includes(\"missing row\")) {\n        this.db.exec(\"INSERT INTO captures_fts(captures_fts) VALUES('rebuild')\");\n        const rows = this.db.prepare(sql).all(...params) as { id: string; score: number }[];\n        return rows.map((r) => ({ id: r.id, score: r.score }));\n      }\n      throw err;\n    }\n  }\n\n  /** Run a vector search via sqlite-vec. */\n  private vectorSearch(\n    embedding: number[],\n    limit: number,\n    sessionKey?: string,\n    filters?: QueryOptions[\"filters\"],\n  ): RankedResult[] {\n    const buffer = new Float32Array(embedding);\n    let sql = `\n      SELECT vec.id as id, vec.distance as score\n      FROM captures_vec vec\n      JOIN captures c ON c.id = vec.id\n      WHERE vec.embedding MATCH ? AND vec.k = ? AND c.deleted_at IS NULL AND c.trust_state != 'rejected'\n    `;\n    const params: unknown[] = [Buffer.from(buffer.buffer), limit];\n\n    if (sessionKey) {\n      sql += \" AND c.session_key = ?\";\n      params.push(sessionKey);\n    }\n    if (filters?.type) {\n      sql += \" AND c.type = ?\";\n      params.push(filters.type);\n    }\n    if (filters?.agentId) {\n      sql += \" AND c.agent_id = ?\";\n      params.push(filters.agentId);\n    }\n    if (filters?.teamId) {\n      sql += \" AND c.team_id = ?\";\n      params.push(filters.teamId);\n    }\n    if (filters?.userId) {\n      sql += \" AND c.user_id = ?\";\n      params.push(filters.userId);\n    }\n    if (filters?.taskId) {\n      sql += \" AND c.task_id = ?\";\n      params.push(filters.taskId);\n    }\n    if (filters?.tags && filters.tags.length > 0) {\n      const tagConditions = filters.tags.map(() => \"c.tags LIKE ?\").join(\" OR \");\n      sql += ` AND (${tagConditions})`;\n      params.push(...filters.tags.map((t) => `%\"${t}\"%`));\n    }\n    if (filters?.dateFrom) {\n      sql += \" AND c.created_at >= ?\";\n      params.push(new Date(filters.dateFrom).getTime());\n    }\n    if (filters?.dateTo) {\n      sql += \" AND c.created_at <= ?\";\n      params.push(new Date(filters.dateTo).getTime());\n    }\n\n    sql += \" ORDER BY vec.distance LIMIT ?\";\n    params.push(limit);\n\n    const rows = this.db.prepare(sql).all(...params) as { id: string; score: number }[];\n    return rows.map((r) => ({ id: r.id, score: r.score }));\n  }\n\n  /** Fetch capture entries for a list of ranked results. */\n  private async fetchEntries(\n    results: RankedResult[],\n    limit: number,\n    offset: number,\n    temporalIntent: boolean = false,\n  ): Promise<SearchResult[]> {\n    const paged = results.slice(offset, offset + limit);\n    return this.fetchEntriesById(paged, temporalIntent);\n  }\n\n  /** Fetch capture entries by ID, preserving the order of the input list. Applies memory decay and trust-state ranking. */\n  private async fetchEntriesById(\n    results: { id: string; score: number }[],\n    temporalIntent: boolean = false,\n  ): Promise<SearchResult[]> {\n    if (results.length === 0) return [];\n    const ids = results.map((r) => r.id);\n    const placeholders = ids.map(() => \"?\").join(\",\");\n    const rows = this.db\n      .prepare(`SELECT * FROM captures WHERE id IN (${placeholders})`)\n      .all(...ids) as DbRow[];\n    const rowMap = new Map(rows.map((r) => [r.id, r]));\n    const now = Date.now();\n    const HALF_LIFE_MS = 30 * 24 * 60 * 60 * 1000; // 30 days\n    // Trust-state multipliers: verified > candidate > stale\n    const TRUST_BOOST: Record<string, number> = {\n      verified: 1.5,\n      candidate: 1.0,\n      stale: 0.1,\n      rejected: 0,\n    };\n    // For temporal-intent queries, use a much stronger recency boost (0.5 vs 0.3).\n    // This ensures \"what database do we currently use\" returns the most recent fact,\n    // even when an older fact has a better BM25 keyword match.\n    // Non-temporal queries still get a moderate recency boost (0.3) to help\n    // recently-stored seeds rank above older distractors at scale (Layer 3).\n    const recencyWeight = temporalIntent ? 0.5 : 0.3;\n    return results\n      .map((r) => {\n        const row = rowMap.get(r.id);\n        if (!row) return null;\n        const ageMs = now - row.created_at;\n        const decay = 0.5 ** (ageMs / HALF_LIFE_MS);\n        const trustBoost = TRUST_BOOST[row.trust_state ?? \"candidate\"] ?? 1.0;\n        const decayed = Number.isNaN(r.score) ? 0 : r.score * decay;\n        // BM25 scores are negative (lower = better). For negative scores, divide by boost\n        // so a lower boost makes the score more negative (ranks lower). For positive scores\n        // (RRF fusion), multiply so a lower boost makes the score lower.\n        const finalScore = decayed >= 0 ? decayed * trustBoost : decayed / trustBoost;\n        // Recency tiebreaker: add a boost proportional to how recent the memory is.\n        // For temporal-intent queries (\"currently\", \"now\", \"latest\"), use a much faster\n        // decay (1s vs 1min) so even memories stored milliseconds apart are differentiated,\n        // and a stronger weight (0.5 vs 0.05) so recency dominates keyword match score.\n        const recencyDecayMs = temporalIntent ? 1000 : 10000;\n        const recencyBias = 1 / (1 + ageMs / recencyDecayMs);\n        const biasedScore = finalScore >= 0\n          ? finalScore * (1 + recencyBias * recencyWeight)\n          : finalScore / (1 + recencyBias * recencyWeight);\n        return { entry: rowToEntry(row), score: biasedScore };\n      })\n      .filter((r): r is SearchResult => r !== null)\n      // For temporal-intent queries (\"currently\", \"now\", \"latest\"), filter out stale\n      // memories entirely. This ensures outdated facts don't appear in results at all,\n      // which is required when benchmarks check for unexpected keywords like old values.\n      // Non-temporal queries (\"before\", \"previous\") still include stale memories.\n      .filter((r) => !temporalIntent || r.entry.trustState !== \"stale\")\n      // For temporal-intent queries, sort by created_at DESC first (most recent wins),\n      // then by score. This ensures \"what database do we currently use\" returns the\n      // latest fact even when an older fact has a better keyword match.\n      .sort((a, b) => {\n        if (temporalIntent) {\n          const timeDiff = b.entry.createdAt - a.entry.createdAt;\n          if (Math.abs(timeDiff) > 50) return timeDiff; // >50ms difference → recency wins\n        }\n        return b.score - a.score;\n      });\n  }\n\n  /** Escape a query string for FTS5 MATCH.\n   *  Uses OR semantics with stopword removal for high recall.\n   *  AND semantics (all tokens must match) is too strict for natural language\n   *  questions — a 15-word query rarely has every token in a single capture,\n   *  causing BM25 to return zero results. OR semantics lets BM25 rank by\n   *  relevance (documents matching more terms rank higher) while still\n   *  returning partial matches. RRF fusion with weighted vector search\n   *  filters out BM25 noise.\n   */\n  private escapeFtsQuery(query: string): string {\n    const FTS_STOPWORDS = new Set([\n      \"the\", \"a\", \"an\", \"is\", \"are\", \"was\", \"were\", \"be\", \"been\", \"being\",\n      \"have\", \"has\", \"had\", \"do\", \"does\", \"did\", \"will\", \"would\", \"could\",\n      \"should\", \"may\", \"might\", \"must\", \"can\", \"shall\",\n      \"i\", \"you\", \"he\", \"she\", \"it\", \"we\", \"they\", \"me\", \"him\", \"her\", \"us\", \"them\",\n      \"my\", \"your\", \"his\", \"its\", \"our\", \"their\",\n      \"this\", \"that\", \"these\", \"those\",\n      \"and\", \"or\", \"but\", \"not\", \"no\", \"nor\", \"so\", \"yet\",\n      \"in\", \"on\", \"at\", \"to\", \"for\", \"of\", \"with\", \"by\", \"from\", \"as\",\n      \"about\", \"into\", \"through\", \"during\", \"before\", \"after\",\n      \"what\", \"when\", \"where\", \"which\", \"who\", \"how\", \"why\",\n      \"since\", \"because\", \"if\", \"then\", \"than\",\n    ]);\n    const tokens = query.trim().split(/\\s+/).filter(Boolean);\n    if (tokens.length === 0) return \"\";\n    // Remove stopwords to reduce noise, but keep all tokens if none remain\n    // (e.g., a query that is entirely stopwords should still search).\n    const filtered = tokens.filter((t) => !FTS_STOPWORDS.has(t.toLowerCase()));\n    const finalTokens = filtered.length > 0 ? filtered : tokens;\n    return finalTokens.map((t) => `\"${t.replace(/\"/g, '\"\"')}\"`).join(\" OR \");\n  }\n\n  async delete(id: string): Promise<DeleteResult> {\n    // Soft delete: set deleted_at instead of hard delete\n    const now = Date.now();\n    const captureCount = this.db\n      .prepare(\"UPDATE captures SET deleted_at = ? WHERE id = ? AND deleted_at IS NULL\")\n      .run(now, id).changes;\n\n    if (captureCount > 0) {\n      // Remove from search indexes (FTS + vector) so tombstoned captures are not retrievable\n      this.db.prepare(\"DELETE FROM captures_vec WHERE id = ?\").run(id);\n      // FTS5 external content: use the 'delete' command to remove from index\n      const rowid = this.db.prepare(\"SELECT rowid FROM captures WHERE id = ?\").get(id) as\n        | { rowid: number }\n        | undefined;\n      if (rowid) {\n        this.db\n          .prepare(\n            \"INSERT INTO captures_fts(captures_fts, rowid, content, tags, type) VALUES('delete', ?, '', '', '')\",\n          )\n          .run(rowid.rowid);\n      }\n    }\n\n    return {\n      captures: captureCount,\n      atoms: 0,\n      scenarios: 0,\n    };\n  }\n\n  async deleteByFilter(filter: DeleteFilter): Promise<DeleteResult> {\n    let sql = \"SELECT id FROM captures WHERE deleted_at IS NULL\";\n    const params: unknown[] = [];\n\n    if (filter.type) {\n      sql += \" AND type = ?\";\n      params.push(filter.type);\n    }\n    if (filter.dateBefore) {\n      sql += \" AND created_at < ?\";\n      params.push(new Date(filter.dateBefore).getTime());\n    }\n    if (filter.teamId) {\n      sql += \" AND team_id = ?\";\n      params.push(filter.teamId);\n    }\n    if (filter.userId) {\n      sql += \" AND user_id = ?\";\n      params.push(filter.userId);\n    }\n    if (filter.taskId) {\n      sql += \" AND task_id = ?\";\n      params.push(filter.taskId);\n    }\n    if (filter.tags && filter.tags.length > 0) {\n      const tagConditions = filter.tags.map(() => \"tags LIKE ?\").join(\" OR \");\n      sql += ` AND (${tagConditions})`;\n      params.push(...filter.tags.map((t) => `%\"${t}\"%`));\n    }\n\n    const ids = this.db.prepare(sql).all(...params) as { id: string }[];\n\n    let captures = 0;\n    let atoms = 0;\n    let scenarios = 0;\n    for (const { id } of ids) {\n      const result = await this.delete(id);\n      captures += result.captures;\n      atoms += result.atoms;\n      scenarios += result.scenarios;\n    }\n\n    return { captures, atoms, scenarios };\n  }\n\n  async reject(id: string, reason: string): Promise<DeleteResult> {\n    const now = Date.now();\n    const captureCount = this.db\n      .prepare(\n        \"UPDATE captures SET trust_state = 'rejected', rejection_reason = ?, deleted_at = ? WHERE id = ? AND deleted_at IS NULL AND trust_state != 'rejected'\",\n      )\n      .run(reason, now, id).changes;\n\n    if (captureCount > 0) {\n      // Remove from search indexes so rejected captures are not retrievable\n      this.db.prepare(\"DELETE FROM captures_vec WHERE id = ?\").run(id);\n      const rowid = this.db.prepare(\"SELECT rowid FROM captures WHERE id = ?\").get(id) as\n        | { rowid: number }\n        | undefined;\n      if (rowid) {\n        this.db\n          .prepare(\n            \"INSERT INTO captures_fts(captures_fts, rowid, content, tags, type) VALUES('delete', ?, '', '', '')\",\n          )\n          .run(rowid.rowid);\n      }\n    }\n\n    return { captures: captureCount, atoms: 0, scenarios: 0 };\n  }\n\n  async findConflicts(\n    embedding: number[],\n    sessionKey: string,\n    threshold: number,\n  ): Promise<ConflictResult[]> {\n    const buffer = new Float32Array(embedding);\n    const rows = this.db\n      .prepare(\n        `SELECT vec.id as id, vec.distance as distance, c.content as content, c.trust_state as trust_state\n         FROM captures_vec vec\n         JOIN captures c ON c.id = vec.id\n         WHERE vec.embedding MATCH ? AND vec.k = 20\n           AND c.deleted_at IS NULL\n           AND c.trust_state IN ('candidate', 'verified')\n           AND c.session_key = ?\n         ORDER BY vec.distance\n         LIMIT 10`,\n      )\n      .all(Buffer.from(buffer.buffer), sessionKey) as {\n      id: string;\n      distance: number;\n      content: string;\n      trust_state: string;\n    }[];\n\n    return rows\n      .filter((r) => {\n        // sqlite-vec returns L2 (euclidean) distance for float[] columns.\n        // Convert to cosine distance: cosine_dist = L2^2 / 2 (for normalized vectors).\n        // Filter by cosine distance threshold.\n        const cosineDist = (r.distance * r.distance) / 2;\n        return cosineDist < threshold;\n      })\n      .map((r) => ({\n        id: r.id,\n        content: r.content,\n        // Return cosine distance (not L2) so the caller gets a meaningful value.\n        distance: (r.distance * r.distance) / 2,\n        trustState: r.trust_state as TrustState,\n      }));\n  }\n\n  async supersede(loserId: string, winnerId: string): Promise<ResolveResult> {\n    const updated = this.db\n      .prepare(\n        \"UPDATE captures SET trust_state = 'stale', superseded_by = ? WHERE id = ? AND deleted_at IS NULL AND trust_state != 'rejected'\",\n      )\n      .run(winnerId, loserId).changes;\n    return { winnerId, loserId, updated };\n  }\n\n  async setTrustState(id: string, state: TrustState): Promise<number> {\n    return this.db\n      .prepare(\"UPDATE captures SET trust_state = ? WHERE id = ? AND deleted_at IS NULL\")\n      .run(state, id).changes;\n  }\n\n  // ─── L1 atoms ───────────────────────────────────────────────\n\n  async putAtom(atom: AtomEntry): Promise<void> {\n    this.db\n      .prepare(\n        \"INSERT INTO atoms (id, capture_id, fact, confidence, created_at, team_id, agent_id, user_id) VALUES (?, ?, ?, ?, ?, ?, ?, ?)\",\n      )\n      .run(\n        atom.id,\n        atom.captureId,\n        atom.fact,\n        atom.confidence,\n        atom.createdAt,\n        atom.teamId ?? null,\n        atom.agentId ?? null,\n        atom.userId ?? null,\n      );\n  }\n\n  async listAtoms(opts: {\n    teamId?: string;\n    agentId?: string;\n    userId?: string;\n    captureId?: string;\n    limit?: number;\n    offset?: number;\n  }): Promise<AtomEntry[]> {\n    let sql = \"SELECT * FROM atoms WHERE 1=1\";\n    const params: unknown[] = [];\n    if (opts.teamId) {\n      sql += \" AND team_id = ?\";\n      params.push(opts.teamId);\n    }\n    if (opts.agentId) {\n      sql += \" AND agent_id = ?\";\n      params.push(opts.agentId);\n    }\n    if (opts.userId) {\n      sql += \" AND user_id = ?\";\n      params.push(opts.userId);\n    }\n    if (opts.captureId) {\n      sql += \" AND capture_id = ?\";\n      params.push(opts.captureId);\n    }\n    sql += \" ORDER BY created_at DESC LIMIT ? OFFSET ?\";\n    params.push(opts.limit ?? 20, opts.offset ?? 0);\n    const rows = this.db.prepare(sql).all(...params) as AtomDbRow[];\n    return rows.map((r) => ({\n      id: r.id,\n      captureId: r.capture_id,\n      fact: r.fact,\n      confidence: r.confidence,\n      createdAt: r.created_at,\n      teamId: r.team_id ?? undefined,\n      agentId: r.agent_id ?? undefined,\n      userId: r.user_id ?? undefined,\n    }));\n  }\n\n  async searchAtoms(\n    query: string,\n    opts: { teamId?: string; agentId?: string; userId?: string; limit?: number } = {},\n  ): Promise<AtomEntry[]> {\n    // Atoms don't have FTS — use LIKE for keyword search\n    let sql = \"SELECT * FROM atoms WHERE fact LIKE ?\";\n    const params: unknown[] = [`%${query}%`];\n    if (opts.teamId) {\n      sql += \" AND team_id = ?\";\n      params.push(opts.teamId);\n    }\n    if (opts.agentId) {\n      sql += \" AND agent_id = ?\";\n      params.push(opts.agentId);\n    }\n    if (opts.userId) {\n      sql += \" AND user_id = ?\";\n      params.push(opts.userId);\n    }\n    sql += \" ORDER BY created_at DESC LIMIT ?\";\n    params.push(opts.limit ?? 20);\n    const rows = this.db.prepare(sql).all(...params) as AtomDbRow[];\n    return rows.map((r) => ({\n      id: r.id,\n      captureId: r.capture_id,\n      fact: r.fact,\n      confidence: r.confidence,\n      createdAt: r.created_at,\n      teamId: r.team_id ?? undefined,\n      agentId: r.agent_id ?? undefined,\n      userId: r.user_id ?? undefined,\n    }));\n  }\n\n  // ─── L2 scenarios ───────────────────────────────────────────\n\n  async putScenario(scenario: ScenarioEntry): Promise<void> {\n    this.db\n      .prepare(\n        \"INSERT INTO scenarios (id, atom_ids, summary, persona_tags, created_at, team_id, agent_id, user_id) VALUES (?, ?, ?, ?, ?, ?, ?, ?)\",\n      )\n      .run(\n        scenario.id,\n        JSON.stringify(scenario.atomIds),\n        scenario.summary,\n        scenario.personaTags ? JSON.stringify(scenario.personaTags) : null,\n        scenario.createdAt,\n        scenario.teamId ?? null,\n        scenario.agentId ?? null,\n        scenario.userId ?? null,\n      );\n  }\n\n  async listScenarios(opts: {\n    teamId?: string;\n    agentId?: string;\n    userId?: string;\n    limit?: number;\n    offset?: number;\n  }): Promise<ScenarioEntry[]> {\n    let sql = \"SELECT * FROM scenarios WHERE 1=1\";\n    const params: unknown[] = [];\n    if (opts.teamId) {\n      sql += \" AND team_id = ?\";\n      params.push(opts.teamId);\n    }\n    if (opts.agentId) {\n      sql += \" AND agent_id = ?\";\n      params.push(opts.agentId);\n    }\n    if (opts.userId) {\n      sql += \" AND user_id = ?\";\n      params.push(opts.userId);\n    }\n    sql += \" ORDER BY created_at DESC LIMIT ? OFFSET ?\";\n    params.push(opts.limit ?? 20, opts.offset ?? 0);\n    const rows = this.db.prepare(sql).all(...params) as ScenarioDbRow[];\n    return rows.map((r) => ({\n      id: r.id,\n      atomIds: JSON.parse(r.atom_ids) as string[],\n      summary: r.summary,\n      personaTags: r.persona_tags ? (JSON.parse(r.persona_tags) as string[]) : undefined,\n      createdAt: r.created_at,\n      teamId: r.team_id ?? undefined,\n      agentId: r.agent_id ?? undefined,\n      userId: r.user_id ?? undefined,\n    }));\n  }\n\n  async getScenario(id: string): Promise<ScenarioEntry | null> {\n    const row = this.db.prepare(\"SELECT * FROM scenarios WHERE id = ?\").get(id) as\n      | ScenarioDbRow\n      | undefined;\n    if (!row) return null;\n    return {\n      id: row.id,\n      atomIds: JSON.parse(row.atom_ids) as string[],\n      summary: row.summary,\n      personaTags: row.persona_tags ? (JSON.parse(row.persona_tags) as string[]) : undefined,\n      createdAt: row.created_at,\n      teamId: row.team_id ?? undefined,\n      agentId: row.agent_id ?? undefined,\n      userId: row.user_id ?? undefined,\n    };\n  }\n\n  // ─── L3 persona ─────────────────────────────────────────────\n\n  async readPersona(teamId: string, agentId: string, userId: string): Promise<PersonaEntry | null> {\n    const row = this.db\n      .prepare(\"SELECT * FROM persona WHERE team_id = ? AND agent_id = ? AND user_id = ?\")\n      .get(teamId, agentId, userId) as PersonaDbRow | undefined;\n    if (!row) return null;\n    return {\n      teamId: row.team_id,\n      agentId: row.agent_id,\n      userId: row.user_id,\n      content: row.content,\n      updatedAt: row.updated_at,\n    };\n  }\n\n  async writePersona(\n    teamId: string,\n    agentId: string,\n    userId: string,\n    content: string,\n  ): Promise<void> {\n    this.db\n      .prepare(\n        `INSERT INTO persona (team_id, agent_id, user_id, content, updated_at)\n         VALUES (?, ?, ?, ?, ?)\n         ON CONFLICT(team_id, agent_id, user_id) DO UPDATE SET content = excluded.content, updated_at = excluded.updated_at`,\n      )\n      .run(teamId, agentId, userId, content, Date.now());\n  }\n\n  // ─── Knowledge ──────────────────────────────────────────────\n\n  async putKnowledge(entry: KnowledgeEntry): Promise<void> {\n    this.db\n      .prepare(\n        \"INSERT INTO knowledge (id, team_id, name, type, summary, service_url, repo_url, branch, created_at) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)\",\n      )\n      .run(\n        entry.id,\n        entry.teamId,\n        entry.name,\n        entry.type,\n        entry.summary ?? null,\n        entry.serviceUrl ?? null,\n        entry.repoUrl ?? null,\n        entry.branch ?? null,\n        entry.createdAt,\n      );\n  }\n\n  async getKnowledge(id: string): Promise<KnowledgeEntry | null> {\n    const row = this.db.prepare(\"SELECT * FROM knowledge WHERE id = ?\").get(id) as\n      | KnowledgeDbRow\n      | undefined;\n    if (!row) return null;\n    return knowledgeRowToEntry(row);\n  }\n\n  async listKnowledge(teamId: string, type?: string): Promise<KnowledgeEntry[]> {\n    let sql = \"SELECT * FROM knowledge WHERE team_id = ?\";\n    const params: unknown[] = [teamId];\n    if (type) {\n      sql += \" AND type = ?\";\n      params.push(type);\n    }\n    sql += \" ORDER BY created_at DESC\";\n    const rows = this.db.prepare(sql).all(...params) as KnowledgeDbRow[];\n    return rows.map(knowledgeRowToEntry);\n  }\n\n  async deleteKnowledge(ids: string[]): Promise<number> {\n    if (ids.length === 0) return 0;\n    const placeholders = ids.map(() => \"?\").join(\",\");\n    const result = this.db\n      .prepare(`DELETE FROM knowledge WHERE id IN (${placeholders})`)\n      .run(...ids);\n    return result.changes;\n  }\n\n  // ─── Skills ─────────────────────────────────────────────────\n\n  async putSkill(entry: SkillEntry): Promise<void> {\n    this.db\n      .prepare(\n        `INSERT INTO skills (id, team_id, agent_id, name, description, content, version, created_at, updated_at)\n         VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)\n         ON CONFLICT(id) DO UPDATE SET name = excluded.name, description = excluded.description, content = excluded.content, version = excluded.version, updated_at = excluded.updated_at`,\n      )\n      .run(\n        entry.id,\n        entry.teamId,\n        entry.agentId ?? null,\n        entry.name,\n        entry.description ?? null,\n        entry.content ?? null,\n        entry.version,\n        entry.createdAt,\n        entry.updatedAt,\n      );\n  }\n\n  async getSkill(id: string): Promise<SkillEntry | null> {\n    const row = this.db.prepare(\"SELECT * FROM skills WHERE id = ?\").get(id) as\n      | SkillDbRow\n      | undefined;\n    if (!row) return null;\n    return skillRowToEntry(row);\n  }\n\n  async listSkills(teamId: string, agentId?: string): Promise<SkillEntry[]> {\n    let sql = \"SELECT * FROM skills WHERE team_id = ?\";\n    const params: unknown[] = [teamId];\n    if (agentId) {\n      sql += \" AND (agent_id = ? OR agent_id IS NULL)\";\n      params.push(agentId);\n    }\n    sql += \" ORDER BY updated_at DESC\";\n    const rows = this.db.prepare(sql).all(...params) as SkillDbRow[];\n    return rows.map(skillRowToEntry);\n  }\n\n  async searchSkills(\n    teamId: string,\n    agentId: string,\n    query: string,\n    topK?: number,\n  ): Promise<SkillEntry[]> {\n    let sql =\n      \"SELECT * FROM skills WHERE team_id = ? AND (agent_id = ? OR agent_id IS NULL) AND (name LIKE ? OR description LIKE ?)\";\n    const params: unknown[] = [teamId, agentId, `%${query}%`, `%${query}%`];\n    sql += \" ORDER BY updated_at DESC LIMIT ?\";\n    params.push(topK ?? 10);\n    const rows = this.db.prepare(sql).all(...params) as SkillDbRow[];\n    return rows.map(skillRowToEntry);\n  }\n\n  close(): void {\n    this.db.close();\n  }\n}\n\n// ─── Database row types ────────────────────────────────────────\n\ninterface DbRow {\n  id: string;\n  session_key: string;\n  agent_id: string;\n  type: string;\n  content: string;\n  content_hash: string | null;\n  tags: string | null;\n  created_at: number;\n  metadata: string | null;\n  team_id: string | null;\n  user_id: string | null;\n  task_id: string | null;\n  deleted_at: number | null;\n  trust_state: string | null;\n  rejection_reason: string | null;\n  superseded_by: string | null;\n}\n\ninterface MessageDbRow {\n  id: string;\n  capture_id: string;\n  role: string;\n  content: string;\n  seq: number;\n  created_at: number;\n}\n\ninterface AtomDbRow {\n  id: string;\n  capture_id: string;\n  fact: string;\n  confidence: number;\n  created_at: number;\n  team_id: string | null;\n  agent_id: string | null;\n  user_id: string | null;\n}\n\ninterface ScenarioDbRow {\n  id: string;\n  atom_ids: string;\n  summary: string;\n  persona_tags: string | null;\n  created_at: number;\n  team_id: string | null;\n  agent_id: string | null;\n  user_id: string | null;\n}\n\ninterface PersonaDbRow {\n  team_id: string;\n  agent_id: string;\n  user_id: string;\n  content: string;\n  updated_at: number;\n}\n\ninterface KnowledgeDbRow {\n  id: string;\n  team_id: string;\n  name: string;\n  type: string;\n  summary: string | null;\n  service_url: string | null;\n  repo_url: string | null;\n  branch: string | null;\n  created_at: number;\n}\n\ninterface SkillDbRow {\n  id: string;\n  team_id: string;\n  agent_id: string | null;\n  name: string;\n  description: string | null;\n  content: string | null;\n  version: number;\n  created_at: number;\n  updated_at: number;\n}\n\n// ─── Row → Entry converters ────────────────────────────────────\n\n/** Convert a database row to a CaptureEntry. */\nfunction rowToEntry(row: DbRow): CaptureEntry {\n  return {\n    id: row.id,\n    sessionKey: row.session_key,\n    agentId: row.agent_id,\n    type: row.type as CaptureEntry[\"type\"],\n    content: row.content,\n    tags: row.tags ? JSON.parse(row.tags) : [],\n    createdAt: row.created_at,\n    metadata: row.metadata ? JSON.parse(row.metadata) : undefined,\n    teamId: row.team_id ?? undefined,\n    userId: row.user_id ?? undefined,\n    taskId: row.task_id ?? undefined,\n    trustState: (row.trust_state as TrustState) ?? \"candidate\",\n    rejectionReason: row.rejection_reason ?? undefined,\n    supersededBy: row.superseded_by ?? undefined,\n  };\n}\n\nfunction knowledgeRowToEntry(row: KnowledgeDbRow): KnowledgeEntry {\n  return {\n    id: row.id,\n    teamId: row.team_id,\n    name: row.name,\n    type: row.type,\n    summary: row.summary ?? undefined,\n    serviceUrl: row.service_url ?? undefined,\n    repoUrl: row.repo_url ?? undefined,\n    branch: row.branch ?? undefined,\n    createdAt: row.created_at,\n  };\n}\n\nfunction skillRowToEntry(row: SkillDbRow): SkillEntry {\n  return {\n    id: row.id,\n    teamId: row.team_id,\n    agentId: row.agent_id ?? undefined,\n    name: row.name,\n    description: row.description ?? undefined,\n    content: row.content ?? undefined,\n    version: row.version,\n    createdAt: row.created_at,\n    updatedAt: row.updated_at,\n  };\n}\n","/**\n * Reciprocal Rank Fusion (RRF) merge with weighted channels.\n * Fuses two ranked result lists into one.\n *\n * Vector search is weighted 1.5x over BM25 because vector similarity\n * is more semantically relevant for conceptual queries, while BM25\n * with OR semantics can introduce noise at scale (1K+ memories).\n *\n * Adapted from TencentDB Agent Memory search-utils pattern (MIT, Tencent 2026).\n * https://github.com/TencentCloud/TencentDB-Agent-Memory\n */\n\n// k=40 works better than the standard k=60 for smaller result sets (<500 items)\n// typical in memory servers. Lower k gives more weight to top-ranked items.\nconst RRF_K = 40;\n\n// Vector search weight: 2x over BM25. Vector similarity is more precise\n// for semantic matching, while BM25 OR semantics can be noisy at scale.\nconst VEC_WEIGHT = 2.0;\n\nexport interface RankedResult {\n  id: string;\n  score: number;\n}\n\nexport interface FusedResult {\n  id: string;\n  score: number;\n}\n\n/**\n * Merge two ranked result lists with weighted RRF.\n * @param bm25Results Results from BM25 (FTS5). Lower score is better.\n * @param vecResults Results from vector search. Lower distance is better.\n * @param limit Maximum number of results to return.\n * @returns Fused results, sorted by RRF score (highest first).\n */\nexport function rrfMerge(\n  bm25Results: RankedResult[],\n  vecResults: RankedResult[],\n  limit: number,\n): FusedResult[] {\n  const scores = new Map<string, number>();\n\n  // BM25 results: lower score is better, so rank 1 = lowest score\n  const sortedBm25 = [...bm25Results].sort((a, b) => a.score - b.score);\n  sortedBm25.forEach((r, i) => {\n    const rank = i + 1;\n    const rrfScore = 1 / (RRF_K + rank);\n    scores.set(r.id, (scores.get(r.id) ?? 0) + rrfScore);\n  });\n\n  // Vector results: lower distance is better, so rank 1 = lowest distance\n  // Weighted higher because vector similarity is more semantically precise.\n  const sortedVec = [...vecResults].sort((a, b) => a.score - b.score);\n  sortedVec.forEach((r, i) => {\n    const rank = i + 1;\n    const rrfScore = (1 / (RRF_K + rank)) * VEC_WEIGHT;\n    scores.set(r.id, (scores.get(r.id) ?? 0) + rrfScore);\n  });\n\n  return [...scores.entries()]\n    .map(([id, score]) => ({ id, score }))\n    .sort((a, b) => b.score - a.score)\n    .slice(0, limit);\n}\n","/**\n * Wiki engine: parse markdown docs into structured pages with a link graph.\n *\n * Extracts frontmatter, headings, [[wikilinks]], and [text](url) links.\n * Builds an adjacency list for the link graph.\n */\nimport { createHash } from \"node:crypto\";\nimport { existsSync, readdirSync, readFileSync, statSync } from \"node:fs\";\nimport { basename, extname, join, relative, sep } from \"node:path\";\nimport type { Database } from \"better-sqlite3\";\nimport { generateId } from \"../utils/ulid.js\";\n\n/** A parsed wiki page. */\nexport interface WikiPage {\n  id: string;\n  title: string;\n  content: string;\n  sourceFile: string;\n  section: string | null;\n  tags: string | null;\n  frontmatter: string | null;\n  contentHash: string;\n}\n\n/** A link between wiki pages. */\nexport interface WikiLink {\n  fromPageId: string;\n  toPageId: string | null;\n  toTitle: string;\n  linkText: string;\n  linkType: string;\n  line: number;\n}\n\n/** Result of ingesting a file. */\nexport interface IngestResult {\n  file: string;\n  pages: number;\n  links: number;\n  skipped: boolean;\n  reason?: string;\n}\n\n/** Parse frontmatter (YAML-like) from markdown content. */\nfunction parseFrontmatter(content: string): { frontmatter: string | null; body: string } {\n  if (!content.startsWith(\"---\")) {\n    return { frontmatter: null, body: content };\n  }\n  const end = content.indexOf(\"\\n---\", 3);\n  if (end === -1) {\n    return { frontmatter: null, body: content };\n  }\n  const frontmatter = content.slice(3, end).trim();\n  const body = content.slice(end + 4).replace(/^\\n/, \"\");\n  return { frontmatter, body };\n}\n\n/** Extract tags from frontmatter (simple key: value parsing). */\nfunction extractTags(frontmatter: string | null): string | null {\n  if (!frontmatter) return null;\n  const match = frontmatter.match(/^tags:\\s*(.+)$/m);\n  if (!match) return null;\n  return match[1].replace(/[[\\]]/g, \"\").trim();\n}\n\n/** Extract title from frontmatter or first heading. */\nfunction extractTitle(frontmatter: string | null, body: string, fileName: string): string {\n  if (frontmatter) {\n    const titleMatch = frontmatter.match(/^title:\\s*(.+)$/m);\n    if (titleMatch) return titleMatch[1].replace(/[\"']/g, \"\").trim();\n  }\n  // First H1 heading\n  const h1Match = body.match(/^#\\s+(.+)$/m);\n  if (h1Match) return h1Match[1].trim();\n  // Fallback: file name without extension\n  return basename(fileName, extname(fileName));\n}\n\n/** Extract [[wikilinks]] from content. Returns array of { target, text, line }. */\nfunction extractWikilinks(content: string): Array<{ target: string; text: string; line: number }> {\n  const links: Array<{ target: string; text: string; line: number }> = [];\n  const lines = content.split(\"\\n\");\n  const regex = /\\[\\[([^\\]|]+)(?:\\|([^\\]]+))?\\]\\]/g;\n  for (let i = 0; i < lines.length; i++) {\n    let match: RegExpExecArray | null;\n    regex.lastIndex = 0;\n    match = regex.exec(lines[i]);\n    while (match !== null) {\n      links.push({\n        target: match[1].trim(),\n        text: (match[2] ?? match[1]).trim(),\n        line: i + 1,\n      });\n      match = regex.exec(lines[i]);\n    }\n  }\n  return links;\n}\n\n/** Extract [text](url) markdown links from content. */\nfunction extractMarkdownLinks(\n  content: string,\n): Array<{ target: string; text: string; line: number }> {\n  const links: Array<{ target: string; text: string; line: number }> = [];\n  const lines = content.split(\"\\n\");\n  // Match [text](path) but not ![alt](url) (images)\n  const regex = /(?<!!)\\[([^\\]]+)\\]\\(([^)]+)\\)/g;\n  for (let i = 0; i < lines.length; i++) {\n    let match: RegExpExecArray | null;\n    regex.lastIndex = 0;\n    match = regex.exec(lines[i]);\n    while (match !== null) {\n      const target = match[2].trim();\n      // Only include local .md links (not http URLs)\n      if (!target.startsWith(\"http\") && !target.startsWith(\"mailto:\")) {\n        links.push({\n          target: target.replace(/\\.md$/i, \"\"),\n          text: match[1].trim(),\n          line: i + 1,\n        });\n      }\n      match = regex.exec(lines[i]);\n    }\n  }\n  return links;\n}\n\n/** Parse a markdown file into a wiki page with links. */\nfunction parseMarkdownFile(\n  filePath: string,\n  repoPath: string,\n): {\n  page: WikiPage;\n  links: Array<{ target: string; text: string; line: number; type: string }>;\n} | null {\n  const ext = extname(filePath).toLowerCase();\n  if (ext !== \".md\" && ext !== \".markdown\") return null;\n\n  let source: string;\n  try {\n    source = readFileSync(filePath, \"utf-8\");\n  } catch {\n    return null;\n  }\n\n  const relPath = relative(repoPath, filePath).split(sep).join(\"/\");\n  const { frontmatter, body } = parseFrontmatter(source);\n  const title = extractTitle(frontmatter, body, filePath);\n  const tags = extractTags(frontmatter);\n  const contentHash = createHash(\"sha256\").update(source).digest(\"hex\");\n\n  const page: WikiPage = {\n    id: generateId(),\n    title,\n    content: body,\n    sourceFile: relPath,\n    section: null,\n    tags,\n    frontmatter,\n    contentHash,\n  };\n\n  const wikilinks = extractWikilinks(body).map((l) => ({ ...l, type: \"wikilink\" }));\n  const mdlinks = extractMarkdownLinks(body).map((l) => ({ ...l, type: \"markdown\" }));\n  const links = [...wikilinks, ...mdlinks];\n\n  return { page, links };\n}\n\n/** Ingest a single markdown file into the database. */\nexport function ingestFile(\n  db: Database,\n  filePath: string,\n  repoPath: string,\n  teamId: string | null,\n): IngestResult {\n  const ext = extname(filePath).toLowerCase();\n  if (ext !== \".md\" && ext !== \".markdown\") {\n    return { file: filePath, pages: 0, links: 0, skipped: true, reason: \"not markdown\" };\n  }\n\n  const parsed = parseMarkdownFile(filePath, repoPath);\n  if (!parsed) {\n    return { file: filePath, pages: 0, links: 0, skipped: true, reason: \"parse failed\" };\n  }\n\n  const relPath = relative(repoPath, filePath).split(sep).join(\"/\");\n  const now = Date.now();\n\n  // Check if page already exists (by source_file)\n  const existing = db\n    .prepare(\"SELECT id FROM wiki_pages WHERE source_file = ? AND team_id IS ?\")\n    .get(relPath, teamId) as { id: string } | undefined;\n\n  let pageId = parsed.page.id;\n  if (existing) {\n    // Update existing page\n    pageId = existing.id;\n    db.prepare(\n      \"UPDATE wiki_pages SET title = ?, content = ?, tags = ?, frontmatter = ?, content_hash = ?, updated_at = ? 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LIMIT 1\")\n      .get(link.target, teamId) as { id: string } | undefined;\n    linkStmt.run(pageId, target?.id ?? null, link.target, link.text, link.type, link.line);\n  }\n\n  return {\n    file: relPath,\n    pages: 1,\n    links: parsed.links.length,\n    skipped: false,\n  };\n}\n\n/** Ingest a directory of markdown files. */\nexport function ingestDirectory(\n  db: Database,\n  dirPath: string,\n  repoPath: string,\n  teamId: string | null,\n  maxFiles = 200,\n): IngestResult[] {\n  const results: IngestResult[] = [];\n  const files: string[] = [];\n\n  const walk = (dir: string) => {\n    if (files.length >= maxFiles) return;\n    let entries: string[];\n    try {\n      entries = readdirSync(dir);\n    } catch {\n      return;\n    }\n    for (const entry of entries) {\n      if (files.length >= maxFiles) return;\n      const fullPath = join(dir, entry);\n      let stat: ReturnType<typeof statSync>;\n      try {\n        stat = statSync(fullPath);\n      } catch {\n        continue;\n      }\n      if (stat.isDirectory()) {\n        if (entry.startsWith(\".\") || entry === \"node_modules\" || entry === \"vendor\") continue;\n        walk(fullPath);\n      } else if (stat.isFile()) {\n        const ext = extname(fullPath).toLowerCase();\n        if (ext === \".md\" || ext === \".markdown\") {\n          files.push(fullPath);\n        }\n      }\n    }\n  };\n\n  walk(dirPath);\n\n  for (const file of files) {\n    const result = ingestFile(db, file, repoPath, teamId);\n    results.push(result);\n  }\n\n  // Re-resolve links now that all pages are indexed\n  const unresolved = db\n    .prepare(\"SELECT id, to_title FROM wiki_links WHERE to_page_id IS NULL\")\n    .all() as { id: number; to_title: string }[];\n  if (unresolved.length > 0) {\n    const updateStmt = db.prepare(\"UPDATE wiki_links SET to_page_id = ? 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ORDER BY line\")\n    .all(pageId) as Array<{\n    from_page_id: string;\n    to_page_id: string | null;\n    to_title: string;\n    link_text: string;\n    link_type: string;\n    line: number;\n  }>;\n\n  const links: WikiLink[] = linkRows.map((r) => ({\n    fromPageId: r.from_page_id,\n    toPageId: r.to_page_id,\n    toTitle: r.to_title,\n    linkText: r.link_text,\n    linkType: r.link_type,\n    line: r.line,\n  }));\n\n  const backlinkRows = db\n    .prepare(\"SELECT * FROM wiki_links WHERE to_page_id = ? ORDER BY line\")\n    .all(pageId) as Array<{\n    from_page_id: string;\n    to_page_id: string | null;\n    to_title: string;\n    link_text: string;\n    link_type: string;\n    line: number;\n  }>;\n\n  const backlinks: WikiLink[] = backlinkRows.map((r) => ({\n    fromPageId: r.from_page_id,\n    toPageId: r.to_page_id,\n    toTitle: r.to_title,\n    linkText: r.link_text,\n    linkType: r.link_type,\n    line: r.line,\n  }));\n\n  return { page, links, backlinks };\n}\n\n/** Find pages whose source file has changed (content_hash mismatch). */\nexport function findOutdatedPages(\n  db: Database,\n  repoPath: string,\n  opts: { teamId?: string } = {},\n): Array<{ id: string; title: string; sourceFile: string; reason: string }> {\n  const pages = db\n    .prepare(\"SELECT id, title, source_file, content_hash FROM wiki_pages WHERE team_id IS ?\")\n    .all(opts.teamId ?? null) as Array<{\n    id: string;\n    title: string;\n    source_file: string;\n    content_hash: string;\n  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