cognitive-core 0.2.1 → 0.2.2

package/references/minimem/src/minimem.ts

@@ -1,1276 +0,0 @@
-import { randomUUID } from "node:crypto";
-import fs from "node:fs/promises";
-import path from "node:path";
-import { DatabaseSync } from "node:sqlite";
-import chokidar, { type FSWatcher } from "chokidar";
-
-import {
-  buildFileEntry,
-  chunkMarkdown,
-  ensureDir,
-  extractChunkMetadata,
-  hashText,
-  listMemoryFiles,
-  logError,
-  type MemoryChunk,
-  type MemoryFileEntry,
-  parseEmbedding,
-  vectorToBlob,
-} from "./internal.js";
-import { bm25RankToScore, buildFtsQuery, mergeHybridResults } from "./search/hybrid.js";
-import { searchKeyword, searchVector, buildKnowledgeFilterSql } from "./search/search.js";
-import { ensureMemoryIndexSchema } from "./db/schema.js";
-import { parseFrontmatter, type MemoryFrontmatter, type KnowledgeLink } from "./session.js";
-import {
-  getLinksFrom,
-  getLinksTo,
-  getNeighbors,
-  getPathBetween,
-  type GraphLink,
-  type GraphNeighbor,
-} from "./search/graph.js";
-import { loadSqliteVecExtension } from "./db/sqlite-vec.js";
-import {
-  createEmbeddingProvider,
-  type EmbeddingProvider,
-  type EmbeddingProviderOptions,
-  type OpenAiEmbeddingClient,
-  type GeminiEmbeddingClient,
-} from "./embeddings/embeddings.js";
-import { runOpenAiEmbeddingBatches, type OpenAiBatchRequest, OPENAI_BATCH_ENDPOINT } from "./embeddings/batch-openai.js";
-import { runGeminiEmbeddingBatches, type GeminiBatchRequest } from "./embeddings/batch-gemini.js";
-
-const META_KEY = "memory_index_meta_v1";
-const SNIPPET_MAX_CHARS = 700;
-const VECTOR_TABLE = "chunks_vec";
-const FTS_TABLE = "chunks_fts";
-const EMBEDDING_CACHE_TABLE = "embedding_cache";
-const EMBEDDING_BATCH_MAX_TOKENS = 8000;
-const EMBEDDING_APPROX_CHARS_PER_TOKEN = 1;
-const EMBEDDING_INDEX_CONCURRENCY = 4;
-const EMBEDDING_RETRY_MAX_ATTEMPTS = 3;
-const EMBEDDING_RETRY_BASE_DELAY_MS = 500;
-const EMBEDDING_RETRY_MAX_DELAY_MS = 8000;
-const VECTOR_LOAD_TIMEOUT_MS = 30_000;
-const EMBEDDING_QUERY_TIMEOUT_REMOTE_MS = 60_000;
-const EMBEDDING_QUERY_TIMEOUT_LOCAL_MS = 5 * 60_000;
-
-export type MinimemConfig = {
-  /** Directory containing memory files (MEMORY.md, memory/*.md) */
-  memoryDir: string;
-  /** Path to SQLite database. Defaults to memoryDir/.minimem/index.db */
-  dbPath?: string;
-  /** Embedding provider options */
-  embedding: EmbeddingProviderOptions;
-  /** Chunking configuration */
-  chunking?: {
-    /** Tokens per chunk (default: 256) */
-    tokens?: number;
-    /** Overlap tokens between chunks (default: 32) */
-    overlap?: number;
-  };
-  /** Embedding cache configuration */
-  cache?: {
-    /** Enable embedding cache (default: true) */
-    enabled?: boolean;
-    /** Max cache entries before LRU pruning (default: 10000) */
-    maxEntries?: number;
-  };
-  /** Hybrid search configuration */
-  hybrid?: {
-    /** Enable hybrid search (default: true) */
-    enabled?: boolean;
-    /** Weight for vector search (default: 0.7) */
-    vectorWeight?: number;
-    /** Weight for keyword search (default: 0.3) */
-    textWeight?: number;
-    /** Candidate multiplier for search (default: 2.0) */
-    candidateMultiplier?: number;
-  };
-  /** Query configuration */
-  query?: {
-    /** Max results (default: 10) */
-    maxResults?: number;
-    /** Min score threshold (default: 0.3) */
-    minScore?: number;
-  };
-  /** File watching configuration */
-  watch?: {
-    /** Enable file watching (default: true) */
-    enabled?: boolean;
-    /** Debounce delay in ms (default: 1000) */
-    debounceMs?: number;
-  };
-  /** Batch embedding configuration */
-  batch?: {
-    /** Enable batch embedding API (default: false) */
-    enabled?: boolean;
-    /** Wait for batch completion (default: true) */
-    wait?: boolean;
-    /** Concurrent batch requests (default: 2) */
-    concurrency?: number;
-    /** Poll interval in ms (default: 2000) */
-    pollIntervalMs?: number;
-    /** Timeout in ms (default: 60 minutes) */
-    timeoutMs?: number;
-  };
-  /** sqlite-vec extension path (optional) */
-  vectorExtensionPath?: string;
-  /** Debug logging function */
-  debug?: (message: string, data?: Record<string, unknown>) => void;
-};
-
-export type MinimemSearchResult = {
-  path: string;
-  startLine: number;
-  endLine: number;
-  score: number;
-  snippet: string;
-};
-
-type MemoryIndexMeta = {
-  model: string;
-  provider: string;
-  providerKey?: string;
-  chunkTokens: number;
-  chunkOverlap: number;
-  vectorDims?: number;
-};
-
-export class Minimem {
-  private readonly memoryDir: string;
-  private readonly dbPath: string;
-  private readonly chunking: { tokens: number; overlap: number };
-  private readonly cache: { enabled: boolean; maxEntries: number };
-  private readonly hybrid: {
-    enabled: boolean;
-    vectorWeight: number;
-    textWeight: number;
-    candidateMultiplier: number;
-  };
-  private readonly queryConfig: { maxResults: number; minScore: number };
-  private readonly watchConfig: { enabled: boolean; debounceMs: number };
-  private readonly batchConfig: {
-    enabled: boolean;
-    wait: boolean;
-    concurrency: number;
-    pollIntervalMs: number;
-    timeoutMs: number;
-  };
-  private readonly vectorExtensionPath?: string;
-  private readonly debug?: (message: string, data?: Record<string, unknown>) => void;
-
-  private provider!: EmbeddingProvider;
-  private openAi?: OpenAiEmbeddingClient;
-  private gemini?: GeminiEmbeddingClient;
-  private providerKey: string = "";
-  private providerFallbackReason?: string;
-  private db!: DatabaseSync;
-
-  private readonly vector: {
-    enabled: boolean;
-    available: boolean | null;
-    extensionPath?: string;
-    loadError?: string;
-    dims?: number;
-  };
-  private readonly fts: {
-    enabled: boolean;
-    available: boolean;
-    loadError?: string;
-  };
-
-  private vectorReady: Promise<boolean> | null = null;
-  private watcher: FSWatcher | null = null;
-  private watchTimer: NodeJS.Timeout | null = null;
-  private closed = false;
-  private dirty = true;
-  private syncing: Promise<void> | null = null;
-  private syncLock = false;
-  private embeddingOptions: EmbeddingProviderOptions;
-
-  private constructor(config: MinimemConfig) {
-    this.memoryDir = path.resolve(config.memoryDir);
-    this.dbPath = config.dbPath ?? path.join(this.memoryDir, ".minimem", "index.db");
-    this.chunking = {
-      tokens: config.chunking?.tokens ?? 256,
-      overlap: config.chunking?.overlap ?? 32,
-    };
-    this.cache = {
-      enabled: config.cache?.enabled ?? true,
-      maxEntries: config.cache?.maxEntries ?? 10000,
-    };
-    this.hybrid = {
-      enabled: config.hybrid?.enabled ?? true,
-      vectorWeight: config.hybrid?.vectorWeight ?? 0.7,
-      textWeight: config.hybrid?.textWeight ?? 0.3,
-      candidateMultiplier: config.hybrid?.candidateMultiplier ?? 2.0,
-    };
-    this.queryConfig = {
-      maxResults: config.query?.maxResults ?? 10,
-      minScore: config.query?.minScore ?? 0.3,
-    };
-    this.watchConfig = {
-      enabled: config.watch?.enabled ?? true,
-      debounceMs: config.watch?.debounceMs ?? 1000,
-    };
-    this.batchConfig = {
-      enabled: config.batch?.enabled ?? false,
-      wait: config.batch?.wait ?? true,
-      concurrency: config.batch?.concurrency ?? 2,
-      pollIntervalMs: config.batch?.pollIntervalMs ?? 2000,
-      timeoutMs: config.batch?.timeoutMs ?? 60 * 60 * 1000,
-    };
-    this.vectorExtensionPath = config.vectorExtensionPath;
-    this.debug = config.debug;
-    this.embeddingOptions = config.embedding;
-
-    this.vector = {
-      enabled: true,
-      available: null,
-      extensionPath: this.vectorExtensionPath,
-    };
-    this.fts = { enabled: this.hybrid.enabled, available: false };
-  }
-
-  static async create(config: MinimemConfig): Promise<Minimem> {
-    const instance = new Minimem(config);
-    await instance.initialize();
-    return instance;
-  }
-
-  private async initialize(): Promise<void> {
-    // Create embedding provider
-    const providerResult = await createEmbeddingProvider(this.embeddingOptions);
-    this.provider = providerResult.provider;
-    this.openAi = providerResult.openAi;
-    this.gemini = providerResult.gemini;
-    this.providerKey = this.computeProviderKey();
-    this.providerFallbackReason = providerResult.fallbackReason;
-
-    // Log warning if in BM25-only fallback mode
-    if (this.provider.id === "none") {
-      this.debug?.("Running in BM25-only mode (no embedding API available)");
-    }
-
-    // Open database
-    this.db = this.openDatabase();
-    this.ensureSchema();
-
-    // Check for existing vector dims
-    const meta = this.readMeta();
-    if (meta?.vectorDims) {
-      this.vector.dims = meta.vectorDims;
-    }
-
-    // Start file watcher
-    if (this.watchConfig.enabled) {
-      this.ensureWatcher();
-    }
-  }
-
-  private openDatabase(): DatabaseSync {
-    const dbDir = path.dirname(this.dbPath);
-    ensureDir(dbDir);
-    return new DatabaseSync(this.dbPath);
-  }
-
-  private ensureSchema(): void {
-    const result = ensureMemoryIndexSchema({
-      db: this.db,
-      embeddingCacheTable: EMBEDDING_CACHE_TABLE,
-      ftsTable: FTS_TABLE,
-      ftsEnabled: this.fts.enabled,
-    });
-    this.fts.available = result.ftsAvailable;
-    if (result.ftsError) {
-      this.fts.loadError = result.ftsError;
-    }
-  }
-
-  private computeProviderKey(): string {
-    const parts: string[] = [this.provider.id, this.provider.model];
-    if (this.openAi) {
-      parts.push(this.openAi.baseUrl);
-    }
-    if (this.gemini) {
-      parts.push(this.gemini.baseUrl);
-    }
-    return hashText(parts.join(":"));
-  }
-
-  private readMeta(): MemoryIndexMeta | null {
-    try {
-      const row = this.db.prepare(`SELECT value FROM meta WHERE key = ?`).get(META_KEY) as
-        | { value: string }
-        | undefined;
-      if (!row?.value) return null;
-      return JSON.parse(row.value) as MemoryIndexMeta;
-    } catch {
-      return null;
-    }
-  }
-
-  private writeMeta(meta: MemoryIndexMeta): void {
-    this.db
-      .prepare(`INSERT OR REPLACE INTO meta (key, value) VALUES (?, ?)`)
-      .run(META_KEY, JSON.stringify(meta));
-  }
-
-  private ensureWatcher(): void {
-    if (this.watcher) return;
-    const memorySubDir = path.join(this.memoryDir, "memory");
-    const memoryFile = path.join(this.memoryDir, "MEMORY.md");
-
-    this.watcher = chokidar.watch([memoryFile, memorySubDir], {
-      ignoreInitial: true,
-      persistent: true,
-      awaitWriteFinish: { stabilityThreshold: 200, pollInterval: 50 },
-    });
-
-    const scheduleSync = () => {
-      this.dirty = true;
-      if (this.watchTimer) clearTimeout(this.watchTimer);
-      this.watchTimer = setTimeout(() => {
-        void this.sync({ reason: "watch" }).catch((err) => {
-          this.debug?.(`memory sync failed (watch): ${String(err)}`);
-        });
-      }, this.watchConfig.debounceMs);
-    };
-
-    this.watcher.on("add", scheduleSync);
-    this.watcher.on("change", scheduleSync);
-    this.watcher.on("unlink", scheduleSync);
-  }
-
-  /**
-   * Check if the index is stale by comparing file mtimes against stored values.
-   * This is a lightweight check (stat calls only, no file reads).
-   */
-  private async isStale(): Promise<boolean> {
-    try {
-      const files = await listMemoryFiles(this.memoryDir);
-
-      // Get stored file records
-      const stored = this.db
-        .prepare(`SELECT path, mtime FROM files WHERE source = ?`)
-        .all("memory") as Array<{ path: string; mtime: number }>;
-
-      // Quick check: different file count means stale
-      if (files.length !== stored.length) {
-        this.debug?.(`Stale: file count changed (${stored.length} -> ${files.length})`);
-        return true;
-      }
-
-      // Build lookup map of stored mtimes
-      const storedMap = new Map(stored.map((f) => [f.path, f.mtime]));
-
-      // Check each file's mtime against stored value
-      for (const absPath of files) {
-        const relPath = path.relative(this.memoryDir, absPath).replace(/\\/g, "/");
-        const storedMtime = storedMap.get(relPath);
-
-        // File not in index = stale
-        if (storedMtime === undefined) {
-          this.debug?.(`Stale: new file ${relPath}`);
-          return true;
-        }
-
-        // Check mtime
-        const stat = await fs.stat(absPath);
-        const currentMtime = Math.floor(stat.mtimeMs);
-        if (currentMtime !== storedMtime) {
-          this.debug?.(`Stale: mtime changed for ${relPath}`);
-          return true;
-        }
-      }
-
-      return false;
-    } catch (err) {
-      // On error, assume stale to be safe
-      this.debug?.(`Stale check failed: ${String(err)}`);
-      return true;
-    }
-  }
-
-  async search(
-    query: string,
-    opts?: { maxResults?: number; minScore?: number; type?: string },
-  ): Promise<MinimemSearchResult[]> {
-    // Check staleness: use dirty flag if watcher is on, otherwise check mtimes
-    if (this.dirty || (!this.watchConfig.enabled && (await this.isStale()))) {
-      await this.sync({ reason: "search" });
-    }
-
-    const cleaned = query.trim();
-    if (!cleaned) return [];
-
-    const minScore = opts?.minScore ?? this.queryConfig.minScore;
-    const maxResults = opts?.maxResults ?? this.queryConfig.maxResults;
-    const candidates = Math.min(
-      200,
-      Math.max(1, Math.floor(maxResults * this.hybrid.candidateMultiplier)),
-    );
-
-    const sourceFilter = { sql: "", params: [] as string[] };
-
-    const keywordResults = this.hybrid.enabled && this.fts.available
-      ? await searchKeyword({
-          db: this.db,
-          ftsTable: FTS_TABLE,
-          providerModel: this.provider.model,
-          query: cleaned,
-          limit: candidates,
-          snippetMaxChars: SNIPPET_MAX_CHARS,
-          sourceFilter,
-          buildFtsQuery,
-          bm25RankToScore,
-        }).catch(() => [])
-      : [];
-
-    const queryVec = await this.embedQueryWithTimeout(cleaned);
-    const hasVector = queryVec.some((v) => v !== 0);
-    const vectorResults = hasVector
-      ? await searchVector({
-          db: this.db,
-          vectorTable: VECTOR_TABLE,
-          providerModel: this.provider.model,
-          queryVec,
-          limit: candidates,
-          snippetMaxChars: SNIPPET_MAX_CHARS,
-          ensureVectorReady: (dims) => this.ensureVectorReady(dims),
-          sourceFilterVec: sourceFilter,
-          sourceFilterChunks: sourceFilter,
-        }).catch(() => [])
-      : [];
-
-    // Apply type filter if specified
-    const typeFilterFn = opts?.type
-      ? (id: string) => {
-          const row = this.db
-            .prepare(`SELECT type FROM chunks WHERE id = ?`)
-            .get(id) as { type: string | null } | undefined;
-          return row?.type === opts.type;
-        }
-      : undefined;
-
-    if (!this.hybrid.enabled) {
-      let results = vectorResults;
-      if (typeFilterFn) results = results.filter((r) => typeFilterFn(r.id));
-      return results
-        .filter((entry) => entry.score >= minScore)
-        .slice(0, maxResults)
-        .map((r) => ({
-          path: r.path,
-          startLine: r.startLine,
-          endLine: r.endLine,
-          score: r.score,
-          snippet: r.snippet,
-        }));
-    }
-
-    let filteredVector = vectorResults;
-    let filteredKeyword = keywordResults;
-    if (typeFilterFn) {
-      filteredVector = vectorResults.filter((r) => typeFilterFn(r.id));
-      filteredKeyword = keywordResults.filter((r) => typeFilterFn(r.id));
-    }
-
-    const merged = mergeHybridResults({
-      vector: filteredVector.map((r) => ({
-        id: r.id,
-        path: r.path,
-        startLine: r.startLine,
-        endLine: r.endLine,
-        source: r.source,
-        snippet: r.snippet,
-        vectorScore: r.score,
-      })),
-      keyword: filteredKeyword.map((r) => ({
-        id: r.id,
-        path: r.path,
-        startLine: r.startLine,
-        endLine: r.endLine,
-        source: r.source,
-        snippet: r.snippet,
-        textScore: r.textScore,
-      })),
-      vectorWeight: this.hybrid.vectorWeight,
-      textWeight: this.hybrid.textWeight,
-    });
-
-    return merged
-      .filter((entry) => entry.score >= minScore)
-      .slice(0, maxResults)
-      .map((r) => ({
-        path: r.path,
-        startLine: r.startLine,
-        endLine: r.endLine,
-        score: r.score,
-        snippet: r.snippet,
-      }));
-  }
-
-  async sync(opts?: { reason?: string; force?: boolean }): Promise<void> {
-    // If a sync is already running, wait for it instead of starting another
-    if (this.syncing) {
-      await this.syncing;
-      return;
-    }
-
-    // Use a synchronous flag to prevent the race window between
-    // checking this.syncing and assigning to it
-    if (this.syncLock) {
-      return;
-    }
-    this.syncLock = true;
-
-    this.syncing = this.runSync(opts);
-    try {
-      await this.syncing;
-    } finally {
-      this.syncing = null;
-      this.syncLock = false;
-    }
-  }
-
-  private async runSync(opts?: { reason?: string; force?: boolean }): Promise<void> {
-    this.debug?.(`memory sync starting`, { reason: opts?.reason });
-
-    await this.ensureVectorReady();
-    const meta = this.readMeta();
-    const needsFullReindex =
-      opts?.force ||
-      !meta ||
-      meta.model !== this.provider.model ||
-      meta.provider !== this.provider.id ||
-      meta.providerKey !== this.providerKey ||
-      meta.chunkTokens !== this.chunking.tokens ||
-      meta.chunkOverlap !== this.chunking.overlap ||
-      (this.vector.available && !meta?.vectorDims);
-
-    const files = await listMemoryFiles(this.memoryDir);
-    const activePaths = new Set<string>();
-
-    for (const absPath of files) {
-      const entry = await buildFileEntry(absPath, this.memoryDir);
-      activePaths.add(entry.path);
-
-      const record = this.db
-        .prepare(`SELECT hash FROM files WHERE path = ? AND source = ?`)
-        .get(entry.path, "memory") as { hash: string } | undefined;
-
-      if (!needsFullReindex && record?.hash === entry.hash) {
-        continue;
-      }
-
-      await this.indexFile(entry);
-    }
-
-    // Delete stale entries
-    const staleRows = this.db
-      .prepare(`SELECT path FROM files WHERE source = ?`)
-      .all("memory") as Array<{ path: string }>;
-
-    for (const stale of staleRows) {
-      if (activePaths.has(stale.path)) continue;
-      this.db.prepare(`DELETE FROM files WHERE path = ? AND source = ?`).run(stale.path, "memory");
-      try {
-        this.db
-          .prepare(
-            `DELETE FROM ${VECTOR_TABLE} WHERE id IN (SELECT id FROM chunks WHERE path = ? AND source = ?)`,
-          )
-          .run(stale.path, "memory");
-      } catch (err) {
-        logError("deleteStaleVectorEntries", err, this.debug);
-      }
-      this.db.prepare(`DELETE FROM chunks WHERE path = ? AND source = ?`).run(stale.path, "memory");
-      this.db.prepare(`DELETE FROM knowledge_links WHERE source_path = ?`).run(stale.path);
-      if (this.fts.enabled && this.fts.available) {
-        try {
-          this.db
-            .prepare(`DELETE FROM ${FTS_TABLE} WHERE path = ? AND source = ? AND model = ?`)
-            .run(stale.path, "memory", this.provider.model);
-        } catch (err) {
-          logError("deleteStaleFtsEntries", err, this.debug);
-        }
-      }
-    }
-
-    // Write meta
-    this.writeMeta({
-      model: this.provider.model,
-      provider: this.provider.id,
-      providerKey: this.providerKey,
-      chunkTokens: this.chunking.tokens,
-      chunkOverlap: this.chunking.overlap,
-      vectorDims: this.vector.dims,
-    });
-
-    // Prune embedding cache
-    this.pruneEmbeddingCacheIfNeeded();
-
-    this.dirty = false;
-    this.debug?.(`memory sync complete`, { files: files.length });
-  }
-
-  private async indexFile(entry: MemoryFileEntry): Promise<void> {
-    const content = await fs.readFile(entry.absPath, "utf-8");
-    const chunks = chunkMarkdown(content, this.chunking);
-
-    // Extract knowledge frontmatter
-    const { frontmatter } = parseFrontmatter(content);
-    const knowledgeType = frontmatter?.type ?? null;
-    const knowledgeId = frontmatter?.id ?? null;
-    const domains = frontmatter?.domain ?? null;
-    const entities = frontmatter?.entities ?? null;
-    const confidence = frontmatter?.confidence ?? null;
-    const links = frontmatter?.links ?? null;
-
-    // Get embeddings
-    const embeddings = await this.embedChunks(chunks);
-
-    // Update files table
-    this.db
-      .prepare(
-        `INSERT OR REPLACE INTO files (path, source, hash, mtime, size) VALUES (?, ?, ?, ?, ?)`,
-      )
-      .run(entry.path, "memory", entry.hash, Math.floor(entry.mtimeMs), entry.size);
-
-    // Delete old chunks for this file
-    try {
-      this.db
-        .prepare(
-          `DELETE FROM ${VECTOR_TABLE} WHERE id IN (SELECT id FROM chunks WHERE path = ? AND source = ?)`,
-        )
-        .run(entry.path, "memory");
-    } catch (err) {
-      logError("deleteOldVectorChunks", err, this.debug);
-    }
-    this.db.prepare(`DELETE FROM chunks WHERE path = ? AND source = ?`).run(entry.path, "memory");
-    if (this.fts.enabled && this.fts.available) {
-      try {
-        this.db
-          .prepare(`DELETE FROM ${FTS_TABLE} WHERE path = ? AND source = ? AND model = ?`)
-          .run(entry.path, "memory", this.provider.model);
-      } catch (err) {
-        logError("deleteOldFtsChunks", err, this.debug);
-      }
-    }
-
-    // Delete old knowledge links for this file path on re-index
-    this.db.prepare(`DELETE FROM knowledge_links WHERE source_path = ?`).run(entry.path);
-
-    // Insert new chunks
-    const now = Date.now();
-    for (let i = 0; i < chunks.length; i++) {
-      const chunk = chunks[i];
-      const embedding = embeddings[i] ?? [];
-      const chunkId = randomUUID();
-      const meta = extractChunkMetadata(chunk.text);
-
-      this.db
-        .prepare(
-          `INSERT INTO chunks (id, path, source, start_line, end_line, hash, model, text, embedding, updated_at, type, knowledge_type, knowledge_id, domains, entities, confidence)
-           VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`,
-        )
-        .run(
-          chunkId,
-          entry.path,
-          "memory",
-          chunk.startLine,
-          chunk.endLine,
-          chunk.hash,
-          this.provider.model,
-          chunk.text,
-          JSON.stringify(embedding),
-          now,
-          meta.type ?? null,
-          knowledgeType,
-          knowledgeId,
-          domains ? JSON.stringify(domains) : null,
-          entities ? JSON.stringify(entities) : null,
-          confidence,
-        );
-
-      // Insert into vector table if available
-      if (this.vector.available && embedding.length > 0) {
-        if (!this.vector.dims) {
-          this.vector.dims = embedding.length;
-          this.ensureVectorTable(embedding.length);
-        }
-        try {
-          this.db
-            .prepare(`INSERT INTO ${VECTOR_TABLE} (id, embedding) VALUES (?, ?)`)
-            .run(chunkId, vectorToBlob(embedding));
-        } catch (err) {
-          logError("insertVectorChunk", err, this.debug);
-        }
-      }
-
-      // Insert into FTS table if available
-      if (this.fts.enabled && this.fts.available) {
-        try {
-          this.db
-            .prepare(
-              `INSERT INTO ${FTS_TABLE} (text, id, path, source, model, start_line, end_line)
-               VALUES (?, ?, ?, ?, ?, ?, ?)`,
-            )
-            .run(
-              chunk.text,
-              chunkId,
-              entry.path,
-              "memory",
-              this.provider.model,
-              chunk.startLine,
-              chunk.endLine,
-            );
-        } catch (err) {
-          logError("insertFtsChunk", err, this.debug);
-        }
-      }
-    }
-
-    // Upsert knowledge links if present
-    if (links && knowledgeId) {
-      const upsertLink = this.db.prepare(
-        `INSERT OR REPLACE INTO knowledge_links (from_id, to_id, relation, layer, weight, source_path, created_at)
-         VALUES (?, ?, ?, ?, ?, ?, ?)`,
-      );
-      for (const link of links) {
-        upsertLink.run(
-          knowledgeId,
-          link.target,
-          link.relation,
-          link.layer ?? null,
-          0.5,
-          entry.path,
-          now,
-        );
-      }
-    }
-  }
-
-  private async embedChunks(chunks: MemoryChunk[]): Promise<number[][]> {
-    if (chunks.length === 0) return [];
-
-    const hashes = chunks.map((c) => c.hash);
-    const cached = this.loadEmbeddingCache(hashes);
-    const missing: Array<{ index: number; chunk: MemoryChunk }> = [];
-
-    for (let i = 0; i < chunks.length; i++) {
-      if (!cached.has(hashes[i])) {
-        missing.push({ index: i, chunk: chunks[i] });
-      }
-    }
-
-    if (missing.length > 0) {
-      const texts = missing.map((m) => m.chunk.text);
-      const newEmbeddings = await this.embedBatchWithRetry(texts);
-
-      for (let i = 0; i < missing.length; i++) {
-        const hash = missing[i].chunk.hash;
-        const embedding = newEmbeddings[i] ?? [];
-        cached.set(hash, embedding);
-        this.upsertEmbeddingCache(hash, embedding);
-      }
-    }
-
-    return hashes.map((h) => cached.get(h) ?? []);
-  }
-
-  private async embedBatchWithRetry(texts: string[]): Promise<number[][]> {
-    if (texts.length === 0) return [];
-
-    // Try batch API first if enabled
-    if (this.batchConfig.enabled) {
-      try {
-        return await this.embedWithBatchApi(texts);
-      } catch (err) {
-        this.debug?.(`batch embedding failed, falling back to direct: ${String(err)}`);
-      }
-    }
-
-    // Fall back to direct embedding
-    let lastError: Error | null = null;
-    for (let attempt = 0; attempt < EMBEDDING_RETRY_MAX_ATTEMPTS; attempt++) {
-      try {
-        return await this.provider.embedBatch(texts);
-      } catch (err) {
-        lastError = err instanceof Error ? err : new Error(String(err));
-        if (attempt < EMBEDDING_RETRY_MAX_ATTEMPTS - 1) {
-          const delay = Math.min(
-            EMBEDDING_RETRY_MAX_DELAY_MS,
-            EMBEDDING_RETRY_BASE_DELAY_MS * Math.pow(2, attempt),
-          );
-          await new Promise((resolve) => setTimeout(resolve, delay));
-        }
-      }
-    }
-    throw lastError;
-  }
-
-  private async embedWithBatchApi(texts: string[]): Promise<number[][]> {
-    if (this.openAi) {
-      const requests: OpenAiBatchRequest[] = texts.map((text, i) => ({
-        custom_id: `chunk-${i}`,
-        method: "POST",
-        url: OPENAI_BATCH_ENDPOINT,
-        body: { model: this.openAi!.model, input: text },
-      }));
-
-      const results = await runOpenAiEmbeddingBatches({
-        openAi: this.openAi,
-        source: "minimem",
-        requests,
-        wait: this.batchConfig.wait,
-        pollIntervalMs: this.batchConfig.pollIntervalMs,
-        timeoutMs: this.batchConfig.timeoutMs,
-        concurrency: this.batchConfig.concurrency,
-        debug: this.debug,
-      });
-
-      return texts.map((_, i) => results.get(`chunk-${i}`) ?? []);
-    }
-
-    if (this.gemini) {
-      const requests: GeminiBatchRequest[] = texts.map((text, i) => ({
-        custom_id: `chunk-${i}`,
-        content: { parts: [{ text }] },
-        taskType: "RETRIEVAL_DOCUMENT",
-      }));
-
-      const results = await runGeminiEmbeddingBatches({
-        gemini: this.gemini,
-        source: "minimem",
-        requests,
-        wait: this.batchConfig.wait,
-        pollIntervalMs: this.batchConfig.pollIntervalMs,
-        timeoutMs: this.batchConfig.timeoutMs,
-        concurrency: this.batchConfig.concurrency,
-        debug: this.debug,
-      });
-
-      return texts.map((_, i) => results.get(`chunk-${i}`) ?? []);
-    }
-
-    throw new Error("Batch API not available for local embeddings");
-  }
-
-  private async embedQueryWithTimeout(text: string): Promise<number[]> {
-    const timeout =
-      this.provider.id === "local" ? EMBEDDING_QUERY_TIMEOUT_LOCAL_MS : EMBEDDING_QUERY_TIMEOUT_REMOTE_MS;
-
-    const ac = new AbortController();
-    const timer = setTimeout(() => ac.abort(), timeout);
-
-    try {
-      const result = await Promise.race([
-        this.provider.embedQuery(text),
-        new Promise<number[]>((_, reject) => {
-          ac.signal.addEventListener("abort", () =>
-            reject(new Error("embedding query timeout")),
-          );
-        }),
-      ]);
-      return result;
-    } finally {
-      clearTimeout(timer);
-    }
-  }
-
-  private loadEmbeddingCache(hashes: string[]): Map<string, number[]> {
-    const result = new Map<string, number[]>();
-    if (!this.cache.enabled || hashes.length === 0) return result;
-
-    const placeholders = hashes.map(() => "?").join(",");
-    const rows = this.db
-      .prepare(
-        `SELECT hash, embedding FROM ${EMBEDDING_CACHE_TABLE}
-         WHERE provider = ? AND model = ? AND provider_key = ? AND hash IN (${placeholders})`,
-      )
-      .all(this.provider.id, this.provider.model, this.providerKey, ...hashes) as Array<{
-      hash: string;
-      embedding: string;
-    }>;
-
-    const now = Date.now();
-    for (const row of rows) {
-      result.set(row.hash, parseEmbedding(row.embedding));
-      // Touch for LRU
-      this.db
-        .prepare(
-          `UPDATE ${EMBEDDING_CACHE_TABLE} SET updated_at = ?
-           WHERE provider = ? AND model = ? AND provider_key = ? AND hash = ?`,
-        )
-        .run(now, this.provider.id, this.provider.model, this.providerKey, row.hash);
-    }
-
-    return result;
-  }
-
-  private upsertEmbeddingCache(hash: string, embedding: number[]): void {
-    if (!this.cache.enabled) return;
-    const now = Date.now();
-    this.db
-      .prepare(
-        `INSERT OR REPLACE INTO ${EMBEDDING_CACHE_TABLE}
-         (provider, model, provider_key, hash, embedding, dims, updated_at)
-         VALUES (?, ?, ?, ?, ?, ?, ?)`,
-      )
-      .run(
-        this.provider.id,
-        this.provider.model,
-        this.providerKey,
-        hash,
-        JSON.stringify(embedding),
-        embedding.length,
-        now,
-      );
-  }
-
-  private pruneEmbeddingCacheIfNeeded(): void {
-    if (!this.cache.enabled) return;
-    const row = this.db
-      .prepare(`SELECT COUNT(*) as count FROM ${EMBEDDING_CACHE_TABLE}`)
-      .get() as { count: number };
-    if (row.count <= this.cache.maxEntries) return;
-
-    const excess = row.count - this.cache.maxEntries;
-    this.db
-      .prepare(
-        `DELETE FROM ${EMBEDDING_CACHE_TABLE}
-         WHERE rowid IN (
-           SELECT rowid FROM ${EMBEDDING_CACHE_TABLE}
-           ORDER BY updated_at ASC
-           LIMIT ?
-         )`,
-      )
-      .run(excess);
-  }
-
-  private async ensureVectorReady(dimensions?: number): Promise<boolean> {
-    if (this.vector.available === true) return true;
-    if (this.vector.available === false) return false;
-
-    if (!this.vectorReady) {
-      this.vectorReady = this.loadVectorExtension();
-    }
-
-    const ready = await this.vectorReady;
-    if (ready && dimensions && !this.vector.dims) {
-      this.vector.dims = dimensions;
-      this.ensureVectorTable(dimensions);
-    }
-    return ready;
-  }
-
-  private async loadVectorExtension(): Promise<boolean> {
-    const result = await loadSqliteVecExtension({
-      db: this.db,
-      extensionPath: this.vectorExtensionPath,
-    });
-
-    this.vector.available = result.ok;
-    if (result.error) {
-      this.vector.loadError = result.error;
-      this.debug?.(`sqlite-vec load failed: ${result.error}`);
-    }
-    if (result.extensionPath) {
-      this.vector.extensionPath = result.extensionPath;
-    }
-
-    return result.ok;
-  }
-
-  private ensureVectorTable(dimensions: number): void {
-    if (!this.vector.available) return;
-    try {
-      this.db.exec(
-        `CREATE VIRTUAL TABLE IF NOT EXISTS ${VECTOR_TABLE} USING vec0(
-          id TEXT PRIMARY KEY,
-          embedding FLOAT[${dimensions}]
-        )`,
-      );
-    } catch (err) {
-      this.debug?.(`vector table creation failed: ${String(err)}`);
-    }
-  }
-
-  async readFile(relativePath: string): Promise<string | null> {
-    const absPath = path.join(this.memoryDir, relativePath);
-    try {
-      return await fs.readFile(absPath, "utf-8");
-    } catch {
-      return null;
-    }
-  }
-
-  /**
-   * Read specific lines from a memory file
-   */
-  async readLines(
-    relativePath: string,
-    opts?: { from?: number; lines?: number },
-  ): Promise<{ content: string; startLine: number; endLine: number } | null> {
-    const content = await this.readFile(relativePath);
-    if (content === null) return null;
-
-    const allLines = content.split("\n");
-    const from = Math.max(1, opts?.from ?? 1);
-    const lines = opts?.lines ?? allLines.length;
-
-    const startIdx = from - 1;
-    const endIdx = Math.min(startIdx + lines, allLines.length);
-    const selectedLines = allLines.slice(startIdx, endIdx);
-
-    return {
-      content: selectedLines.join("\n"),
-      startLine: from,
-      endLine: startIdx + selectedLines.length,
-    };
-  }
-
-  /**
-   * Write content to a memory file (creates or overwrites)
-   */
-  async writeFile(relativePath: string, content: string): Promise<void> {
-    this.validateMemoryPath(relativePath);
-    const absPath = path.join(this.memoryDir, relativePath);
-    const dir = path.dirname(absPath);
-    await fs.mkdir(dir, { recursive: true });
-    await fs.writeFile(absPath, content, "utf-8");
-    this.dirty = true;
-    this.debug?.(`memory write: ${relativePath}`);
-  }
-
-  /**
-   * Append content to a memory file (creates if doesn't exist)
-   */
-  async appendFile(relativePath: string, content: string): Promise<void> {
-    this.validateMemoryPath(relativePath);
-    const absPath = path.join(this.memoryDir, relativePath);
-    const dir = path.dirname(absPath);
-    await fs.mkdir(dir, { recursive: true });
-
-    // Ensure newline separation
-    let toAppend = content;
-    try {
-      const existing = await fs.readFile(absPath, "utf-8");
-      if (existing.length > 0 && !existing.endsWith("\n")) {
-        toAppend = "\n" + content;
-      }
-    } catch {
-      // File doesn't exist, will be created
-    }
-
-    await fs.appendFile(absPath, toAppend, "utf-8");
-    this.dirty = true;
-    this.debug?.(`memory append: ${relativePath}`);
-  }
-
-  /**
-   * Append content to today's daily log (memory/YYYY-MM-DD.md)
-   */
-  async appendToday(content: string): Promise<string> {
-    const today = new Date().toISOString().split("T")[0]; // YYYY-MM-DD
-    const relativePath = `memory/${today}.md`;
-    await this.appendFile(relativePath, content);
-    return relativePath;
-  }
-
-  /**
-   * List all memory files
-   */
-  async listFiles(): Promise<string[]> {
-    const files = await listMemoryFiles(this.memoryDir);
-    return files.map((f) => path.relative(this.memoryDir, f).replace(/\\/g, "/"));
-  }
-
-  /**
-   * Validate that a path is within allowed memory locations
-   */
-  private validateMemoryPath(relativePath: string): void {
-    const normalized = relativePath.replace(/\\/g, "/").replace(/^\.\//, "");
-
-    // Allow MEMORY.md at root
-    if (normalized === "MEMORY.md" || normalized === "memory.md") {
-      return;
-    }
-
-    // Allow anything under memory/
-    if (normalized.startsWith("memory/") && normalized.endsWith(".md")) {
-      // Prevent path traversal
-      if (normalized.includes("..")) {
-        throw new Error(`Invalid memory path: ${relativePath} (path traversal not allowed)`);
-      }
-      return;
-    }
-
-    throw new Error(
-      `Invalid memory path: ${relativePath}. Must be MEMORY.md or memory/*.md`,
-    );
-  }
-
-  async status(): Promise<{
-    memoryDir: string;
-    dbPath: string;
-    provider: string;
-    model: string;
-    vectorAvailable: boolean;
-    ftsAvailable: boolean;
-    bm25Only: boolean;
-    fallbackReason?: string;
-    fileCount: number;
-    chunkCount: number;
-    cacheCount: number;
-  }> {
-    const fileRow = this.db.prepare(`SELECT COUNT(*) as count FROM files`).get() as { count: number };
-    const chunkRow = this.db.prepare(`SELECT COUNT(*) as count FROM chunks`).get() as { count: number };
-    const cacheRow = this.db
-      .prepare(`SELECT COUNT(*) as count FROM ${EMBEDDING_CACHE_TABLE}`)
-      .get() as { count: number };
-
-    return {
-      memoryDir: this.memoryDir,
-      dbPath: this.dbPath,
-      provider: this.provider.id,
-      model: this.provider.model,
-      vectorAvailable: this.vector.available === true,
-      ftsAvailable: this.fts.available,
-      bm25Only: this.provider.id === "none",
-      fallbackReason: this.providerFallbackReason,
-      fileCount: fileRow.count,
-      chunkCount: chunkRow.count,
-      cacheCount: cacheRow.count,
-    };
-  }
-
-  /**
-   * Search with knowledge metadata filters (domain, entities, confidence, type).
-   * Runs a standard search then post-filters by knowledge columns.
-   */
-  async knowledgeSearch(
-    query: string,
-    opts?: {
-      maxResults?: number;
-      minScore?: number;
-      domain?: string[];
-      entities?: string[];
-      minConfidence?: number;
-      knowledgeType?: string;
-    },
-  ): Promise<MinimemSearchResult[]> {
-    // Ensure index is up to date
-    if (this.dirty || (!this.watchConfig.enabled && (await this.isStale()))) {
-      await this.sync({ reason: "knowledgeSearch" });
-    }
-
-    const cleaned = query.trim();
-    if (!cleaned) return [];
-
-    const minScore = opts?.minScore ?? this.queryConfig.minScore;
-    const maxResults = opts?.maxResults ?? this.queryConfig.maxResults;
-
-    // Build knowledge filter SQL
-    const { sql: knowledgeWhere, params: knowledgeParams } =
-      buildKnowledgeFilterSql({
-        domain: opts?.domain,
-        entities: opts?.entities,
-        minConfidence: opts?.minConfidence,
-        knowledgeType: opts?.knowledgeType,
-      });
-
-    // If no knowledge filters, delegate to regular search
-    if (!knowledgeWhere) {
-      return this.search(query, { maxResults, minScore });
-    }
-
-    // Get all chunk IDs matching knowledge filters
-    const matchingRows = this.db
-      .prepare(
-        `SELECT id FROM chunks c WHERE c.model = ? AND c.source = 'memory'${knowledgeWhere}`,
-      )
-      .all(this.provider.model, ...knowledgeParams) as Array<{ id: string }>;
-
-    const matchingIds = new Set(matchingRows.map((r) => r.id));
-
-    if (matchingIds.size === 0) return [];
-
-    // Run standard search with extra candidates to compensate for filtering
-    const overFetch = Math.max(maxResults * 3, 30);
-    const results = await this.search(query, {
-      maxResults: overFetch,
-      minScore,
-    });
-
-    // Post-filter: look up chunk IDs for each result and keep only matching ones
-    const filtered: MinimemSearchResult[] = [];
-    for (const r of results) {
-      const row = this.db
-        .prepare(
-          `SELECT id FROM chunks WHERE path = ? AND start_line = ? AND end_line = ? AND model = ?`,
-        )
-        .get(r.path, r.startLine, r.endLine, this.provider.model) as { id: string } | undefined;
-      if (row && matchingIds.has(row.id)) {
-        filtered.push(r);
-        if (filtered.length >= maxResults) break;
-      }
-    }
-
-    return filtered;
-  }
-
-  /**
-   * Get knowledge graph links from or to a node.
-   */
-  getLinks(
-    nodeId: string,
-    direction: "from" | "to" = "from",
-    opts?: { relation?: string; layer?: string },
-  ): GraphLink[] {
-    if (direction === "from") {
-      return getLinksFrom(this.db, nodeId, opts);
-    }
-    return getLinksTo(this.db, nodeId, opts);
-  }
-
-  /**
-   * Get neighbor nodes via BFS traversal.
-   */
-  getGraphNeighbors(
-    nodeId: string,
-    depth: number = 1,
-    opts?: { relation?: string; layer?: string },
-  ): GraphNeighbor[] {
-    return getNeighbors(this.db, nodeId, depth, opts);
-  }
-
-  /**
-   * Find shortest path between two knowledge nodes.
-   */
-  getGraphPath(fromId: string, toId: string, maxDepth: number = 3): GraphLink[] {
-    return getPathBetween(this.db, fromId, toId, maxDepth);
-  }
-
-  close(): void {
-    if (this.closed) return;
-    this.closed = true;
-
-    if (this.watchTimer) {
-      clearTimeout(this.watchTimer);
-      this.watchTimer = null;
-    }
-
-    if (this.watcher) {
-      void this.watcher.close();
-      this.watcher = null;
-    }
-
-    try {
-      this.db.close();
-    } catch (err) {
-      logError("dbClose", err, this.debug);
-    }
-  }
-}