@monoes/monomindcli 1.14.7 → 1.15.1

package/dist/src/memory/memory-initializer.js

@@ -10,7 +10,6 @@
  */
 import * as fs from 'fs';
 import * as path from 'path';
-import { safeParseEmbedding } from './memory-bridge.js';
 /** Maximum SQLite database file size accepted before read (256 MB). */
 const MAX_DB_FILE_BYTES = 256 * 1024 * 1024;
 // ADR-053: Lazy import of AgentDB v1 bridge
@@ -29,675 +28,22 @@ async function getBridge() {
         return null;
     }
 }
-/**
- * Enhanced schema with pattern confidence, temporal decay, versioning
- * Vector embeddings enabled for semantic search
- */
-export const MEMORY_SCHEMA = `
--- Monomind Memory Database
--- Version: 3.0.0
--- Features: Pattern learning, vector embeddings, temporal decay, migration tracking
-
-PRAGMA journal_mode = WAL;
-PRAGMA synchronous = NORMAL;
-PRAGMA foreign_keys = ON;
-
--- ============================================
--- CORE MEMORY TABLES
--- ============================================
-
--- Memory entries (main storage)
-CREATE TABLE IF NOT EXISTS memory_entries (
-  id TEXT PRIMARY KEY,
-  key TEXT NOT NULL,
-  namespace TEXT DEFAULT 'default',
-  content TEXT NOT NULL,
-  type TEXT DEFAULT 'semantic' CHECK(type IN ('semantic', 'episodic', 'procedural', 'working', 'pattern')),
-
-  -- Vector embedding for semantic search (stored as JSON array)
-  embedding TEXT,
-  embedding_model TEXT DEFAULT 'local',
-  embedding_dimensions INTEGER,
-
-  -- Metadata
-  tags TEXT, -- JSON array
-  metadata TEXT, -- JSON object
-  owner_id TEXT,
-
-  -- Timestamps
-  created_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000),
-  updated_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000),
-  expires_at INTEGER,
-  last_accessed_at INTEGER,
-
-  -- Access tracking for hot/cold detection
-  access_count INTEGER DEFAULT 0,
-
-  -- Status
-  status TEXT DEFAULT 'active' CHECK(status IN ('active', 'archived', 'deleted')),
-
-  UNIQUE(namespace, key)
-);
-
--- Indexes for memory entries
-CREATE INDEX IF NOT EXISTS idx_memory_namespace ON memory_entries(namespace);
-CREATE INDEX IF NOT EXISTS idx_memory_key ON memory_entries(key);
-CREATE INDEX IF NOT EXISTS idx_memory_type ON memory_entries(type);
-CREATE INDEX IF NOT EXISTS idx_memory_status ON memory_entries(status);
-CREATE INDEX IF NOT EXISTS idx_memory_created ON memory_entries(created_at);
-CREATE INDEX IF NOT EXISTS idx_memory_accessed ON memory_entries(last_accessed_at);
-CREATE INDEX IF NOT EXISTS idx_memory_owner ON memory_entries(owner_id);
-
--- ============================================
--- PATTERN LEARNING TABLES
--- ============================================
-
--- Learned patterns with confidence scoring and versioning
-CREATE TABLE IF NOT EXISTS patterns (
-  id TEXT PRIMARY KEY,
-
-  -- Pattern identification
-  name TEXT NOT NULL,
-  pattern_type TEXT NOT NULL CHECK(pattern_type IN (
-    'task-routing', 'error-recovery', 'optimization', 'learning',
-    'coordination', 'prediction', 'code-pattern', 'workflow'
-  )),
-
-  -- Pattern definition
-  condition TEXT NOT NULL, -- Regex or semantic match
-  action TEXT NOT NULL, -- What to do when pattern matches
-  description TEXT,
-
-  -- Confidence scoring (0.0 - 1.0)
-  confidence REAL DEFAULT 0.5,
-  success_count INTEGER DEFAULT 0,
-  failure_count INTEGER DEFAULT 0,
-
-  -- Temporal decay
-  decay_rate REAL DEFAULT 0.01, -- How fast confidence decays
-  half_life_days INTEGER DEFAULT 30, -- Days until confidence halves without use
-
-  -- Vector embedding for semantic pattern matching
-  embedding TEXT,
-  embedding_dimensions INTEGER,
-
-  -- Versioning
-  version INTEGER DEFAULT 1,
-  parent_id TEXT REFERENCES patterns(id),
-
-  -- Metadata
-  tags TEXT, -- JSON array
-  metadata TEXT, -- JSON object
-  source TEXT, -- Where the pattern was learned from
-
-  -- Timestamps
-  created_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000),
-  updated_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000),
-  last_matched_at INTEGER,
-  last_success_at INTEGER,
-  last_failure_at INTEGER,
-
-  -- Status
-  status TEXT DEFAULT 'active' CHECK(status IN ('active', 'archived', 'deprecated', 'experimental'))
-);
-
--- Indexes for patterns
-CREATE INDEX IF NOT EXISTS idx_patterns_type ON patterns(pattern_type);
-CREATE INDEX IF NOT EXISTS idx_patterns_confidence ON patterns(confidence DESC);
-CREATE INDEX IF NOT EXISTS idx_patterns_status ON patterns(status);
-CREATE INDEX IF NOT EXISTS idx_patterns_last_matched ON patterns(last_matched_at);
-
--- Pattern evolution history (for versioning)
-CREATE TABLE IF NOT EXISTS pattern_history (
-  id INTEGER PRIMARY KEY AUTOINCREMENT,
-  pattern_id TEXT NOT NULL REFERENCES patterns(id),
-  version INTEGER NOT NULL,
-
-  -- Snapshot of pattern state
-  confidence REAL,
-  success_count INTEGER,
-  failure_count INTEGER,
-  condition TEXT,
-  action TEXT,
-
-  -- What changed
-  change_type TEXT CHECK(change_type IN ('created', 'updated', 'success', 'failure', 'decay', 'merged', 'split')),
-  change_reason TEXT,
-
-  created_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000)
-);
-
-CREATE INDEX IF NOT EXISTS idx_pattern_history_pattern ON pattern_history(pattern_id);
-
--- ============================================
--- LEARNING & TRAJECTORY TABLES
--- ============================================
-
--- Learning trajectories (SONA integration)
-CREATE TABLE IF NOT EXISTS trajectories (
-  id TEXT PRIMARY KEY,
-  session_id TEXT,
-
-  -- Trajectory state
-  status TEXT DEFAULT 'active' CHECK(status IN ('active', 'completed', 'failed', 'abandoned')),
-  verdict TEXT CHECK(verdict IN ('success', 'failure', 'partial', NULL)),
-
-  -- Context
-  task TEXT,
-  context TEXT, -- JSON object
-
-  -- Metrics
-  total_steps INTEGER DEFAULT 0,
-  total_reward REAL DEFAULT 0,
-
-  -- Timestamps
-  started_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000),
-  ended_at INTEGER,
-
-  -- Reference to extracted pattern (if any)
-  extracted_pattern_id TEXT REFERENCES patterns(id)
-);
-
--- Trajectory steps
-CREATE TABLE IF NOT EXISTS trajectory_steps (
-  id INTEGER PRIMARY KEY AUTOINCREMENT,
-  trajectory_id TEXT NOT NULL REFERENCES trajectories(id),
-  step_number INTEGER NOT NULL,
-
-  -- Step data
-  action TEXT NOT NULL,
-  observation TEXT,
-  reward REAL DEFAULT 0,
-
-  -- Metadata
-  metadata TEXT, -- JSON object
-
-  created_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000)
-);
-
-CREATE INDEX IF NOT EXISTS idx_steps_trajectory ON trajectory_steps(trajectory_id);
-
--- ============================================
--- MIGRATION STATE TRACKING
--- ============================================
-
--- Migration state (for resume capability)
-CREATE TABLE IF NOT EXISTS migration_state (
-  id TEXT PRIMARY KEY,
-  migration_type TEXT NOT NULL, -- 'v2-to-v1', 'pattern', 'memory', etc.
-
-  -- Progress tracking
-  status TEXT DEFAULT 'pending' CHECK(status IN ('pending', 'in_progress', 'completed', 'failed', 'rolled_back')),
-  total_items INTEGER DEFAULT 0,
-  processed_items INTEGER DEFAULT 0,
-  failed_items INTEGER DEFAULT 0,
-  skipped_items INTEGER DEFAULT 0,
-
-  -- Current position (for resume)
-  current_batch INTEGER DEFAULT 0,
-  last_processed_id TEXT,
-
-  -- Source/destination info
-  source_path TEXT,
-  source_type TEXT,
-  destination_path TEXT,
-
-  -- Backup info
-  backup_path TEXT,
-  backup_created_at INTEGER,
-
-  -- Error tracking
-  last_error TEXT,
-  errors TEXT, -- JSON array of errors
-
-  -- Timestamps
-  started_at INTEGER,
-  completed_at INTEGER,
-  created_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000),
-  updated_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000)
-);
-
--- ============================================
--- SESSION MANAGEMENT
--- ============================================
-
--- Sessions for context persistence
-CREATE TABLE IF NOT EXISTS sessions (
-  id TEXT PRIMARY KEY,
-
-  -- Session state
-  state TEXT NOT NULL, -- JSON object with full session state
-  status TEXT DEFAULT 'active' CHECK(status IN ('active', 'paused', 'completed', 'expired')),
-
-  -- Context
-  project_path TEXT,
-  branch TEXT,
-
-  -- Metrics
-  tasks_completed INTEGER DEFAULT 0,
-  patterns_learned INTEGER DEFAULT 0,
-
-  -- Timestamps
-  created_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000),
-  updated_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000),
-  expires_at INTEGER
-);
-
--- ============================================
--- VECTOR INDEX METADATA (for HNSW)
--- ============================================
-
--- Track HNSW index state
-CREATE TABLE IF NOT EXISTS vector_indexes (
-  id TEXT PRIMARY KEY,
-  name TEXT NOT NULL UNIQUE,
-
-  -- Index configuration
-  dimensions INTEGER NOT NULL,
-  metric TEXT DEFAULT 'cosine' CHECK(metric IN ('cosine', 'euclidean', 'dot')),
-
-  -- HNSW parameters
-  hnsw_m INTEGER DEFAULT 16,
-  hnsw_ef_construction INTEGER DEFAULT 200,
-  hnsw_ef_search INTEGER DEFAULT 100,
-
-  -- Quantization
-  quantization_type TEXT CHECK(quantization_type IN ('none', 'scalar', 'product')),
-  quantization_bits INTEGER DEFAULT 8,
-
-  -- Statistics
-  total_vectors INTEGER DEFAULT 0,
-  last_rebuild_at INTEGER,
-
-  created_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000),
-  updated_at INTEGER NOT NULL DEFAULT (strftime('%s', 'now') * 1000)
-);
-
--- ============================================
--- SYSTEM METADATA
--- ============================================
-
-CREATE TABLE IF NOT EXISTS metadata (
-  key TEXT PRIMARY KEY,
-  value TEXT NOT NULL,
-  updated_at INTEGER DEFAULT (strftime('%s', 'now') * 1000)
-);
-`;
-let hnswIndex = null;
-let hnswInitializing = false;
-/**
- * Get or create the HNSW index singleton
- * Lazily initializes from SQLite data on first use
- */
-export async function getHNSWIndex(options) {
-    const dimensions = options?.dimensions ?? 384;
-    // Return existing index if already initialized
-    if (hnswIndex?.initialized && !options?.forceRebuild) {
-        return hnswIndex;
-    }
-    // Prevent concurrent initialization
-    if (hnswInitializing) {
-        // Wait for initialization to complete (max 5s)
-        let waitIterations = 0;
-        while (hnswInitializing && waitIterations < 500) {
-            await new Promise(resolve => setTimeout(resolve, 10));
-            waitIterations++;
-        }
-        if (hnswInitializing) {
-            throw new Error('HNSW initialization timed out after 5s');
-        }
-        // Init may have failed — return null rather than a non-initialized index object
-        return hnswIndex?.initialized ? hnswIndex : null;
-    }
-    hnswInitializing = true;
-    try {
-        // Native @monoes/core HNSW (WASM VectorDb) was removed in the lean teardown.
-        // This function is kept for callers that check its return value — all callers
-        // already handle null by falling back to the pure-JS / brute-force path.
-        // The AgentDB bridge (memory-bridge.ts) provides HNSW via agentdb instead.
-        // Native backend removed — return null so callers use the pure-JS fallback.
-        hnswInitializing = false;
-        return null;
-    }
-    catch {
-        hnswInitializing = false;
-        return null;
-    }
-}
-/**
- * Save HNSW metadata to disk for persistence
- */
-function saveHNSWMetadata() {
-    if (!hnswIndex?.entries)
-        return;
-    try {
-        const swarmDir = path.join(process.cwd(), '.swarm');
-        const metadataPath = path.join(swarmDir, 'hnsw.metadata.json');
-        const metadata = Array.from(hnswIndex.entries.entries());
-        const tmp = metadataPath + '.tmp';
-        fs.writeFileSync(tmp, JSON.stringify(metadata));
-        fs.renameSync(tmp, metadataPath);
-    }
-    catch {
-        // Silently fail - metadata save is best-effort
-    }
-}
-/**
- * Add entry to HNSW index (with automatic persistence)
- */
-export async function addToHNSWIndex(id, embedding, entry) {
-    // ADR-053: Try AgentDB v1 bridge first
-    const bridge = await getBridge();
-    if (bridge) {
-        const bridgeResult = await bridge.bridgeAddToHNSW(id, embedding, entry);
-        if (bridgeResult === true)
-            return true;
-    }
-    const index = await getHNSWIndex({ dimensions: embedding.length });
-    if (!index)
-        return false;
-    try {
-        const vector = new Float32Array(embedding);
-        await index.db.insert({
-            id,
-            vector
-        });
-        index.entries.set(id, entry);
-        // Save metadata for persistence (debounced would be better for high-volume)
-        saveHNSWMetadata();
-        return true;
-    }
-    catch {
-        return false;
-    }
-}
-/**
- * Search HNSW index (150x faster than brute-force)
- * Returns results sorted by similarity (highest first)
- */
-export async function searchHNSWIndex(queryEmbedding, options) {
-    // ADR-053: Try AgentDB v1 bridge first
-    const bridge = await getBridge();
-    if (bridge) {
-        const bridgeResult = await bridge.bridgeSearchHNSW(queryEmbedding, options);
-        if (bridgeResult)
-            return bridgeResult;
-    }
-    const index = await getHNSWIndex({ dimensions: queryEmbedding.length });
-    if (!index)
-        return null;
-    try {
-        const vector = new Float32Array(queryEmbedding);
-        const k = options?.k ?? 10;
-        // HNSW search returns results with cosine distance (lower = more similar)
-        const results = await index.db.search({ vector, k: k * 2 }); // Get extra for filtering
-        const filtered = [];
-        for (const result of results) {
-            const entry = index.entries.get(result.id);
-            if (!entry)
-                continue;
-            // Filter by namespace if specified
-            if (options?.namespace && options.namespace !== 'all' && entry.namespace !== options.namespace) {
-                continue;
-            }
-            // Convert cosine distance to similarity score (1 - distance)
-            // Cosine distance convention: 0 = identical, 2 = opposite
-            const score = 1 - (result.score / 2);
-            filtered.push({
-                id: entry.id.substring(0, 12),
-                key: entry.key || entry.id.substring(0, 15),
-                content: entry.content.substring(0, 60) + (entry.content.length > 60 ? '...' : ''),
-                score,
-                namespace: entry.namespace
-            });
-            if (filtered.length >= k)
-                break;
-        }
-        // Sort by score descending (highest similarity first)
-        filtered.sort((a, b) => b.score - a.score);
-        return filtered;
-    }
-    catch {
-        return null;
-    }
-}
-/**
- * Get HNSW index status
- */
-export function getHNSWStatus() {
-    // ADR-053: If bridge was previously loaded, report availability
-    if (_bridge && _bridge !== null) {
-        // Bridge is loaded — HNSW-equivalent is available via AgentDB v1
-        return {
-            available: true,
-            initialized: true,
-            entryCount: hnswIndex?.entries.size ?? 0,
-            dimensions: hnswIndex?.dimensions ?? 384
-        };
-    }
-    return {
-        available: hnswIndex !== null,
-        initialized: hnswIndex?.initialized ?? false,
-        entryCount: hnswIndex?.entries.size ?? 0,
-        dimensions: hnswIndex?.dimensions ?? 384
-    };
-}
-/**
- * Clear the HNSW index (for rebuilding)
- */
-export function clearHNSWIndex() {
-    hnswIndex = null;
-}
-/**
- * Invalidate the in-memory HNSW cache so the next search rebuilds from DB.
- * Call this after deleting entries that had embeddings to prevent ghost
- * vectors from appearing in search results.
- */
-export function rebuildSearchIndex() {
-    hnswIndex = null;
-    hnswInitializing = false;
-}
 // ============================================================================
-// INT8 VECTOR QUANTIZATION (4x memory reduction)
+// Re-exports from extracted modules (ARCH-4)
 // ============================================================================
-/**
- * Quantize a Float32 embedding to Int8 (4x memory reduction)
- * Uses symmetric quantization with scale factor stored per-vector
- *
- * @param embedding - Float32 embedding array
- * @returns Quantized Int8 array with scale factor
- */
-export function quantizeInt8(embedding) {
-    const arr = embedding instanceof Float32Array ? embedding : new Float32Array(embedding);
-    // Find min/max for symmetric quantization
-    let min = Infinity, max = -Infinity;
-    for (let i = 0; i < arr.length; i++) {
-        if (arr[i] < min)
-            min = arr[i];
-        if (arr[i] > max)
-            max = arr[i];
-    }
-    // Symmetric quantization: scale = max(|min|, |max|) / 127
-    const absMax = Math.max(Math.abs(min), Math.abs(max));
-    const scale = absMax / 127 || 1e-10; // Avoid division by zero
-    const zeroPoint = 0; // Symmetric quantization
-    // Quantize
-    const quantized = new Int8Array(arr.length);
-    for (let i = 0; i < arr.length; i++) {
-        // Clamp to [-127, 127] to leave room for potential rounding
-        const q = Math.round(arr[i] / scale);
-        quantized[i] = Math.max(-127, Math.min(127, q));
-    }
-    return { quantized, scale, zeroPoint };
-}
-/**
- * Dequantize Int8 back to Float32
- *
- * @param quantized - Int8 quantized array
- * @param scale - Scale factor from quantization
- * @param zeroPoint - Zero point (usually 0 for symmetric)
- * @returns Float32Array
- */
-export function dequantizeInt8(quantized, scale, zeroPoint = 0) {
-    const result = new Float32Array(quantized.length);
-    for (let i = 0; i < quantized.length; i++) {
-        result[i] = (quantized[i] - zeroPoint) * scale;
-    }
-    return result;
-}
-/**
- * Compute cosine similarity between quantized vectors
- * Faster than dequantizing first
- */
-export function quantizedCosineSim(a, aScale, b, bScale) {
-    if (a.length !== b.length)
-        return 0;
-    let dot = 0, normA = 0, normB = 0;
-    for (let i = 0; i < a.length; i++) {
-        dot += a[i] * b[i];
-        normA += a[i] * a[i];
-        normB += b[i] * b[i];
-    }
-    // Scales cancel out in cosine similarity for normalized vectors
-    const mag = Math.sqrt(normA * normB);
-    return mag === 0 ? 0 : dot / mag;
-}
-/**
- * Get quantization statistics for an embedding
- */
-export function getQuantizationStats(embedding) {
-    const len = embedding.length;
-    const originalBytes = len * 4; // Float32 = 4 bytes
-    const quantizedBytes = len + 8; // Int8 = 1 byte + 8 bytes for scale/zeroPoint
-    const compressionRatio = originalBytes / quantizedBytes;
-    return { originalBytes, quantizedBytes, compressionRatio };
-}
+export { MEMORY_SCHEMA } from './memory-schema.js';
+export { getHNSWIndex, addToHNSWIndex, searchHNSWIndex, getHNSWStatus, clearHNSWIndex, rebuildSearchIndex, quantizeInt8, dequantizeInt8, quantizedCosineSim, getQuantizationStats, batchCosineSim, softmaxAttention, topKIndices, flashAttentionSearch, } from './hnsw-operations.js';
+export { ensureSchemaColumns, checkAndMigrateLegacy, } from './memory-migrations.js';
+export { loadEmbeddingModel, generateEmbedding, generateBatchEmbeddings, generateHashEmbedding, } from './embedding-operations.js';
+export { verifyMemoryInit, storeEntry, searchEntries, listEntries, getEntry, deleteEntry, } from './memory-crud.js';
 // ============================================================================
-// FLASH ATTENTION-STYLE BATCH OPERATIONS (V8-Optimized)
+// Local imports for use in this file
 // ============================================================================
-/**
- * Batch cosine similarity - compute query against multiple vectors
- * Optimized for V8 JIT with typed arrays
- * ~50μs per 1000 vectors (384-dim)
- */
-export function batchCosineSim(query, vectors) {
-    const n = vectors.length;
-    const scores = new Float32Array(n);
-    if (n === 0 || query.length === 0)
-        return scores;
-    // Pre-compute query norm
-    let queryNorm = 0;
-    for (let i = 0; i < query.length; i++) {
-        queryNorm += query[i] * query[i];
-    }
-    queryNorm = Math.sqrt(queryNorm);
-    if (queryNorm === 0)
-        return scores;
-    // Compute similarities
-    for (let v = 0; v < n; v++) {
-        const vec = vectors[v];
-        const len = Math.min(query.length, vec.length);
-        let dot = 0, vecNorm = 0;
-        for (let i = 0; i < len; i++) {
-            dot += query[i] * vec[i];
-            vecNorm += vec[i] * vec[i];
-        }
-        vecNorm = Math.sqrt(vecNorm);
-        scores[v] = vecNorm === 0 ? 0 : dot / (queryNorm * vecNorm);
-    }
-    return scores;
-}
-/**
- * Softmax normalization for attention scores
- * Numerically stable implementation
- */
-export function softmaxAttention(scores, temperature = 1.0) {
-    const n = scores.length;
-    const result = new Float32Array(n);
-    if (n === 0)
-        return result;
-    // Find max for numerical stability
-    let max = scores[0];
-    for (let i = 1; i < n; i++) {
-        if (scores[i] > max)
-            max = scores[i];
-    }
-    // Compute exp and sum
-    let sum = 0;
-    for (let i = 0; i < n; i++) {
-        result[i] = Math.exp((scores[i] - max) / temperature);
-        sum += result[i];
-    }
-    // Normalize
-    if (sum > 0) {
-        for (let i = 0; i < n; i++) {
-            result[i] /= sum;
-        }
-    }
-    return result;
-}
-/**
- * Top-K selection with partial sort (O(n + k log k))
- * More efficient than full sort for small k
- */
-export function topKIndices(scores, k) {
-    const n = scores.length;
-    if (k >= n) {
-        // Return all indices sorted by score
-        return Array.from({ length: n }, (_, i) => i)
-            .sort((a, b) => scores[b] - scores[a]);
-    }
-    // Build min-heap of size k
-    const heap = [];
-    for (let i = 0; i < n; i++) {
-        if (heap.length < k) {
-            heap.push({ idx: i, score: scores[i] });
-            // Bubble up
-            let j = heap.length - 1;
-            while (j > 0) {
-                const parent = Math.floor((j - 1) / 2);
-                if (heap[j].score < heap[parent].score) {
-                    [heap[j], heap[parent]] = [heap[parent], heap[j]];
-                    j = parent;
-                }
-                else
-                    break;
-            }
-        }
-        else if (scores[i] > heap[0].score) {
-            // Replace min and heapify down
-            heap[0] = { idx: i, score: scores[i] };
-            let j = 0;
-            while (true) {
-                const left = 2 * j + 1, right = 2 * j + 2;
-                let smallest = j;
-                if (left < k && heap[left].score < heap[smallest].score)
-                    smallest = left;
-                if (right < k && heap[right].score < heap[smallest].score)
-                    smallest = right;
-                if (smallest === j)
-                    break;
-                [heap[j], heap[smallest]] = [heap[smallest], heap[j]];
-                j = smallest;
-            }
-        }
-    }
-    // Extract and sort descending
-    return heap.sort((a, b) => b.score - a.score).map(h => h.idx);
-}
-/**
- * Flash Attention-style search
- * Combines batch similarity, softmax, and top-k in one pass.
- * Returns indices and attention weights.
- */
-export function flashAttentionSearch(query, vectors, options = {}) {
-    const { k = 10, temperature = 1.0, threshold = 0 } = options;
-    const scores = batchCosineSim(query, vectors);
-    const indices = topKIndices(scores, k).filter(i => scores[i] >= threshold);
-    const topScores = new Float32Array(indices.map(i => scores[i]));
-    const weights = softmaxAttention(topScores, temperature);
-    return { indices, scores: topScores, weights };
-}
+import { MEMORY_SCHEMA } from './memory-schema.js';
+import { checkAndMigrateLegacy, ensureSchemaColumns } from './memory-migrations.js';
+import { rebuildSearchIndex } from './hnsw-operations.js';
+import { verifyMemoryInit, storeEntry, searchEntries, listEntries, getEntry, deleteEntry, } from './memory-crud.js';
+import { loadEmbeddingModel, generateEmbedding, } from './embedding-operations.js';
 // ============================================================================
 // METADATA AND INITIALIZATION
 // ============================================================================
@@ -718,133 +64,14 @@ INSERT OR REPLACE INTO metadata (key, value) VALUES
   ('hnsw_indexing', 'enabled');
 
 -- Create default vector index configuration
+-- Dimensions match BRIDGE_EMBEDDING_DIMS=384 (Xenova/all-MiniLM-L6-v2).
+-- 768 was a legacy value from the agentic-flow era; 384 is the actual
+-- embedding size used by memory-bridge.ts and AgentDB v1.
 INSERT OR IGNORE INTO vector_indexes (id, name, dimensions) VALUES
-  ('default', 'default', 768),
-  ('patterns', 'patterns', 768);
+  ('default', 'default', 384),
+  ('patterns', 'patterns', 384);
 `;
 }
-/**
- * Ensure memory_entries table has all required columns
- * Adds missing columns for older databases (e.g., 'content' column)
- */
-export async function ensureSchemaColumns(dbPath) {
-    const columnsAdded = [];
-    try {
-        if (!fs.existsSync(dbPath)) {
-            return { success: true, columnsAdded: [] };
-        }
-        const initSqlJs = (await import('sql.js')).default;
-        const SQL = await initSqlJs();
-        // Guard against excessively large DB files to prevent OOM.
-        const ensureStat = fs.statSync(dbPath);
-        if (ensureStat.size > MAX_DB_FILE_BYTES) {
-            return { success: false, columnsAdded, error: `Database file too large: ${ensureStat.size} bytes` };
-        }
-        const fileBuffer = fs.readFileSync(dbPath);
-        const db = new SQL.Database(fileBuffer);
-        // Get current columns in memory_entries
-        const tableInfo = db.exec("PRAGMA table_info(memory_entries)");
-        const existingColumns = new Set(tableInfo[0]?.values?.map(row => row[1]) || []);
-        // Required columns that may be missing in older schemas
-        // Issue #977: 'type' column was missing from this list, causing store failures on older DBs
-        const requiredColumns = [
-            { name: 'content', definition: "content TEXT DEFAULT ''" },
-            { name: 'type', definition: "type TEXT DEFAULT 'semantic'" },
-            { name: 'embedding', definition: 'embedding TEXT' },
-            { name: 'embedding_model', definition: "embedding_model TEXT DEFAULT 'local'" },
-            { name: 'embedding_dimensions', definition: 'embedding_dimensions INTEGER' },
-            { name: 'tags', definition: 'tags TEXT' },
-            { name: 'metadata', definition: 'metadata TEXT' },
-            { name: 'owner_id', definition: 'owner_id TEXT' },
-            { name: 'expires_at', definition: 'expires_at INTEGER' },
-            { name: 'last_accessed_at', definition: 'last_accessed_at INTEGER' },
-            { name: 'access_count', definition: 'access_count INTEGER DEFAULT 0' },
-            { name: 'status', definition: "status TEXT DEFAULT 'active'" }
-        ];
-        let modified = false;
-        for (const col of requiredColumns) {
-            if (!existingColumns.has(col.name)) {
-                try {
-                    db.run(`ALTER TABLE memory_entries ADD COLUMN ${col.definition}`);
-                    columnsAdded.push(col.name);
-                    modified = true;
-                }
-                catch (e) {
-                    // Column might already exist or other error - continue
-                }
-            }
-        }
-        if (modified) {
-            // Save updated database (atomic to avoid corruption on crash)
-            const data = db.export();
-            const tmp = dbPath + '.tmp';
-            fs.writeFileSync(tmp, Buffer.from(data));
-            fs.renameSync(tmp, dbPath);
-        }
-        db.close();
-        return { success: true, columnsAdded };
-    }
-    catch (error) {
-        return {
-            success: false,
-            columnsAdded,
-            error: error instanceof Error ? error.message : String(error)
-        };
-    }
-}
-/**
- * Check for legacy database installations and migrate if needed
- */
-export async function checkAndMigrateLegacy(options) {
-    const { dbPath, verbose = false } = options;
-    // Check for legacy locations
-    const legacyPaths = [
-        path.join(process.cwd(), 'memory.db'),
-        path.join(process.cwd(), '.claude/memory.db'),
-        path.join(process.cwd(), 'data/memory.db'),
-        path.join(process.cwd(), '.monomind/memory.db')
-    ];
-    for (const legacyPath of legacyPaths) {
-        if (fs.existsSync(legacyPath) && legacyPath !== dbPath) {
-            try {
-                const initSqlJs = (await import('sql.js')).default;
-                const SQL = await initSqlJs();
-                // Guard against excessively large legacy DB files to prevent OOM.
-                const legacyStat = fs.statSync(legacyPath);
-                if (legacyStat.size > MAX_DB_FILE_BYTES) {
-                    if (verbose) {
-                        console.warn(`[memory] Skipping legacy DB at ${legacyPath}: file too large (${legacyStat.size} bytes)`);
-                    }
-                    continue;
-                }
-                const legacyBuffer = fs.readFileSync(legacyPath);
-                const legacyDb = new SQL.Database(legacyBuffer);
-                // Check if it has data
-                const countResult = legacyDb.exec('SELECT COUNT(*) FROM memory_entries');
-                const count = countResult[0]?.values[0]?.[0] || 0;
-                // Get version if available
-                let version = 'unknown';
-                try {
-                    const versionResult = legacyDb.exec("SELECT value FROM metadata WHERE key='schema_version'");
-                    version = versionResult[0]?.values[0]?.[0] || 'unknown';
-                }
-                catch { /* no metadata table */ }
-                legacyDb.close();
-                if (count > 0) {
-                    return {
-                        needsMigration: true,
-                        legacyVersion: version,
-                        legacyEntries: count
-                    };
-                }
-            }
-            catch {
-                // Not a valid SQLite database, skip
-            }
-        }
-    }
-    return { needsMigration: false };
-}
 /**
  * ADR-053: Activate ControllerRegistry so AgentDB v1 controllers
  * (ReasoningBank, SkillLibrary, ExplainableRecall, etc.) are instantiated.
@@ -1184,1010 +411,6 @@ export async function applyTemporalDecay(dbPath) {
         };
     }
 }
-let embeddingModelState = null;
-/**
- * Lazy load ONNX embedding model
- * Only loads when first embedding is requested
- */
-export async function loadEmbeddingModel(options) {
-    const { verbose = false } = options || {};
-    const startTime = Date.now();
-    // Already loaded
-    if (embeddingModelState?.loaded) {
-        return {
-            success: true,
-            dimensions: embeddingModelState.dimensions,
-            modelName: 'cached',
-            loadTime: 0
-        };
-    }
-    // ADR-053: Try AgentDB v1 bridge first
-    const bridge = await getBridge();
-    if (bridge) {
-        const bridgeResult = await bridge.bridgeLoadEmbeddingModel();
-        if (bridgeResult && bridgeResult.success) {
-            // Mark local state as loaded too so subsequent calls use cache
-            embeddingModelState = {
-                loaded: true,
-                model: null, // Bridge handles embedding
-                tokenizer: null,
-                dimensions: bridgeResult.dimensions
-            };
-            return bridgeResult;
-        }
-    }
-    try {
-        // Try to import @xenova/transformers for ONNX embeddings
-        const transformers = await import('@xenova/transformers').catch(() => null);
-        if (transformers) {
-            if (verbose) {
-                console.log('Loading ONNX embedding model (all-MiniLM-L6-v2)...');
-            }
-            // Use small, fast model for local embeddings
-            const { pipeline } = transformers;
-            const embedder = await pipeline('feature-extraction', 'Xenova/all-MiniLM-L6-v2');
-            embeddingModelState = {
-                loaded: true,
-                model: embedder,
-                tokenizer: null,
-                dimensions: 384 // MiniLM-L6 produces 384-dim vectors
-            };
-            return {
-                success: true,
-                dimensions: 384,
-                modelName: 'Xenova/all-MiniLM-L6-v2',
-                loadTime: Date.now() - startTime
-            };
-        }
-        // Fallback: Check for agentic-flow ReasoningBank embeddings (v1)
-        const reasoningBank = await import('agentic-flow/reasoningbank').catch(() => null);
-        if (reasoningBank?.computeEmbedding) {
-            if (verbose) {
-                console.log('Loading agentic-flow ReasoningBank embedding model...');
-            }
-            embeddingModelState = {
-                loaded: true,
-                model: { embed: reasoningBank.computeEmbedding },
-                tokenizer: null,
-                dimensions: 768
-            };
-            return {
-                success: true,
-                dimensions: 768,
-                modelName: 'agentic-flow/reasoningbank',
-                loadTime: Date.now() - startTime
-            };
-        }
-        // Fallback: Check for monovector ONNX embedder (bundled MiniLM-L6-v2 since v0.2.15)
-        // v0.2.16: LoRA B=0 fix makes AdaptiveEmbedder safe (identity when untrained)
-        // Note: isReady() returns false until first embed() call (lazy init), so we
-        // skip the isReady() gate and verify with a probe embed instead.
-        const monovector = await import('monovector').catch(() => null);
-        if (monovector?.initOnnxEmbedder) {
-            try {
-                await monovector.initOnnxEmbedder();
-                // Fallback: OptimizedOnnxEmbedder (raw ONNX, lazy-inits on first embed)
-                const onnxEmb = monovector.getOptimizedOnnxEmbedder?.();
-                if (onnxEmb?.embed) {
-                    // Probe embed to trigger lazy ONNX init and verify it works
-                    const probe = await onnxEmb.embed('test');
-                    if (probe && probe.length > 0 && (Array.isArray(probe) ? probe.some((v) => v !== 0) : true)) {
-                        if (verbose) {
-                            console.log(`Loading monovector ONNX embedder (all-MiniLM-L6-v2, ${probe.length}d)...`);
-                        }
-                        embeddingModelState = {
-                            loaded: true,
-                            model: (text) => onnxEmb.embed(text),
-                            tokenizer: null,
-                            dimensions: probe.length || 384
-                        };
-                        return {
-                            success: true,
-                            dimensions: probe.length || 384,
-                            modelName: 'monovector/onnx',
-                            loadTime: Date.now() - startTime
-                        };
-                    }
-                }
-            }
-            catch {
-                // monovector ONNX init failed, continue to next fallback
-            }
-        }
-        // Legacy fallback: Check for agentic-flow core embeddings
-        const agenticFlow = await import('agentic-flow').catch(() => null);
-        if (agenticFlow && agenticFlow.embeddings) {
-            if (verbose) {
-                console.log('Loading agentic-flow embedding model...');
-            }
-            embeddingModelState = {
-                loaded: true,
-                model: agenticFlow.embeddings,
-                tokenizer: null,
-                dimensions: 768
-            };
-            return {
-                success: true,
-                dimensions: 768,
-                modelName: 'agentic-flow',
-                loadTime: Date.now() - startTime
-            };
-        }
-        // No ONNX model available - use fallback
-        embeddingModelState = {
-            loaded: true,
-            model: null, // Will use simple hash-based fallback
-            tokenizer: null,
-            dimensions: 128 // Smaller fallback dimensions
-        };
-        return {
-            success: true,
-            dimensions: 128,
-            modelName: 'hash-fallback',
-            loadTime: Date.now() - startTime
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            dimensions: 0,
-            modelName: 'none',
-            error: error instanceof Error ? error.message : String(error)
-        };
-    }
-}
-/**
- * Generate real embedding for text
- * Uses ONNX model if available, falls back to deterministic hash
- */
-export async function generateEmbedding(text) {
-    // Cap input text — caller may pass arbitrarily large content. Without this
-    // cap, the hash-fallback below burns O(text.length × dimension) sin() calls
-    // per call, and ONNX tokenization can saturate memory on multi-MB inputs.
-    if (typeof text !== 'string')
-        text = String(text ?? '');
-    if (text.length > 16 * 1024)
-        text = text.slice(0, 16 * 1024);
-    // ADR-053: Try AgentDB v1 bridge first
-    const bridge = await getBridge();
-    if (bridge) {
-        const bridgeResult = await bridge.bridgeGenerateEmbedding(text);
-        if (bridgeResult)
-            return bridgeResult;
-    }
-    // Ensure model is loaded
-    if (!embeddingModelState?.loaded) {
-        await loadEmbeddingModel();
-    }
-    const state = embeddingModelState;
-    // Use ONNX model if available
-    if (state.model && typeof state.model === 'function') {
-        try {
-            const output = await state.model(text, { pooling: 'mean', normalize: true });
-            // Handle both @xenova/transformers (output.data) and monovector (plain array) formats
-            const embedding = output?.data
-                ? Array.from(output.data)
-                : Array.isArray(output) ? output : null;
-            if (embedding) {
-                return {
-                    embedding,
-                    dimensions: embedding.length,
-                    model: 'onnx'
-                };
-            }
-        }
-        catch {
-            // Fall through to fallback
-        }
-    }
-    // Deterministic hash-based fallback (for testing/demo without ONNX)
-    const embedding = generateHashEmbedding(text, state.dimensions);
-    return {
-        embedding,
-        dimensions: state.dimensions,
-        model: 'hash-fallback'
-    };
-}
-/**
- * Generate embeddings for multiple texts
- * Uses parallel execution for API-based providers (2-4x faster)
- * Note: Local ONNX inference is CPU-bound, so parallelism has limited benefit
- *
- * @param texts - Array of texts to embed
- * @param options - Batch options
- * @returns Array of embedding results with timing info
- */
-export async function generateBatchEmbeddings(texts, options) {
-    const { concurrency = texts.length, onProgress } = options || {};
-    const startTime = Date.now();
-    // Ensure model is loaded first (prevents cold start in parallel)
-    if (!embeddingModelState?.loaded) {
-        await loadEmbeddingModel();
-    }
-    // Process in parallel with optional concurrency limit
-    if (concurrency >= texts.length) {
-        // Full parallelism
-        const embeddings = await Promise.all(texts.map(async (text, i) => {
-            const result = await generateEmbedding(text);
-            onProgress?.(i + 1, texts.length);
-            return { text, ...result };
-        }));
-        const totalTime = Date.now() - startTime;
-        return {
-            results: embeddings,
-            totalTime,
-            avgTime: totalTime / texts.length
-        };
-    }
-    // Limited concurrency using chunking
-    const results = [];
-    let completed = 0;
-    for (let i = 0; i < texts.length; i += concurrency) {
-        const chunk = texts.slice(i, i + concurrency);
-        const chunkResults = await Promise.all(chunk.map(async (text) => {
-            const result = await generateEmbedding(text);
-            completed++;
-            onProgress?.(completed, texts.length);
-            return { text, ...result };
-        }));
-        results.push(...chunkResults);
-    }
-    const totalTime = Date.now() - startTime;
-    return {
-        results,
-        totalTime,
-        avgTime: totalTime / texts.length
-    };
-}
-/**
- * Generate deterministic hash-based embedding
- * Not semantic, but deterministic and useful for testing
- */
-function generateHashEmbedding(text, dimensions) {
-    const embedding = new Array(dimensions).fill(0);
-    // Simple hash-based approach for reproducibility
-    const words = text.toLowerCase().split(/\s+/);
-    for (let i = 0; i < words.length; i++) {
-        const word = words[i];
-        for (let j = 0; j < word.length; j++) {
-            const charCode = word.charCodeAt(j);
-            const idx = (charCode * (i + 1) * (j + 1)) % dimensions;
-            embedding[idx] += Math.sin(charCode * 0.1) * 0.1;
-        }
-    }
-    // Normalize to unit vector
-    const magnitude = Math.sqrt(embedding.reduce((sum, v) => sum + v * v, 0)) || 1;
-    return embedding.map(v => v / magnitude);
-}
-/**
- * Verify memory initialization works correctly
- * Tests: write, read, search, patterns
- */
-export async function verifyMemoryInit(dbPath, options) {
-    const { verbose = false } = options || {};
-    const tests = [];
-    try {
-        const initSqlJs = (await import('sql.js')).default;
-        const SQL = await initSqlJs();
-        const fs = await import('fs');
-        // Guard against excessively large DB files to prevent OOM.
-        const verifyStat = fs.statSync(dbPath);
-        if (verifyStat.size > MAX_DB_FILE_BYTES) {
-            return { success: false, tests: [{ name: 'Database access', passed: false, details: `File too large: ${verifyStat.size} bytes` }], summary: { passed: 0, failed: 1, total: 1 } };
-        }
-        // Load database
-        const fileBuffer = fs.readFileSync(dbPath);
-        const db = new SQL.Database(fileBuffer);
-        // Test 1: Schema verification
-        const schemaStart = Date.now();
-        const tables = db.exec("SELECT name FROM sqlite_master WHERE type='table'");
-        const tableNames = tables[0]?.values?.map(v => v[0]) || [];
-        const expectedTables = ['memory_entries', 'patterns', 'metadata', 'vector_indexes'];
-        const missingTables = expectedTables.filter(t => !tableNames.includes(t));
-        tests.push({
-            name: 'Schema verification',
-            passed: missingTables.length === 0,
-            details: missingTables.length > 0 ? `Missing: ${missingTables.join(', ')}` : `${tableNames.length} tables found`,
-            duration: Date.now() - schemaStart
-        });
-        // Test 2: Write entry
-        const writeStart = Date.now();
-        const testId = `test_${Date.now()}`;
-        const testKey = 'verification_test';
-        const testValue = 'This is a verification test entry for memory initialization';
-        try {
-            db.run(`
-        INSERT INTO memory_entries (id, key, namespace, content, type, created_at, updated_at)
-        VALUES (?, ?, 'test', ?, 'semantic', ?, ?)
-      `, [testId, testKey, testValue, Date.now(), Date.now()]);
-            tests.push({
-                name: 'Write entry',
-                passed: true,
-                details: 'Entry written successfully',
-                duration: Date.now() - writeStart
-            });
-        }
-        catch (e) {
-            tests.push({
-                name: 'Write entry',
-                passed: false,
-                details: e instanceof Error ? e.message : 'Write failed',
-                duration: Date.now() - writeStart
-            });
-        }
-        // Test 3: Read entry
-        const readStart = Date.now();
-        try {
-            const result = db.exec(`SELECT content FROM memory_entries WHERE id = ?`, [testId]);
-            const content = result[0]?.values[0]?.[0];
-            tests.push({
-                name: 'Read entry',
-                passed: content === testValue,
-                details: content === testValue ? 'Content matches' : 'Content mismatch',
-                duration: Date.now() - readStart
-            });
-        }
-        catch (e) {
-            tests.push({
-                name: 'Read entry',
-                passed: false,
-                details: e instanceof Error ? e.message : 'Read failed',
-                duration: Date.now() - readStart
-            });
-        }
-        // Test 4: Write with embedding
-        const embeddingStart = Date.now();
-        try {
-            const { embedding, dimensions, model } = await generateEmbedding(testValue);
-            const embeddingJson = JSON.stringify(embedding);
-            db.run(`
-        UPDATE memory_entries
-        SET embedding = ?, embedding_dimensions = ?, embedding_model = ?
-        WHERE id = ?
-      `, [embeddingJson, dimensions, model, testId]);
-            tests.push({
-                name: 'Generate embedding',
-                passed: true,
-                details: `${dimensions}-dim vector (${model})`,
-                duration: Date.now() - embeddingStart
-            });
-        }
-        catch (e) {
-            tests.push({
-                name: 'Generate embedding',
-                passed: false,
-                details: e instanceof Error ? e.message : 'Embedding failed',
-                duration: Date.now() - embeddingStart
-            });
-        }
-        // Test 5: Pattern storage
-        const patternStart = Date.now();
-        try {
-            const patternId = `pattern_${Date.now()}`;
-            db.run(`
-        INSERT INTO patterns (id, name, pattern_type, condition, action, confidence, created_at, updated_at)
-        VALUES (?, 'test-pattern', 'task-routing', 'test condition', 'test action', 0.5, ?, ?)
-      `, [patternId, Date.now(), Date.now()]);
-            tests.push({
-                name: 'Pattern storage',
-                passed: true,
-                details: 'Pattern stored with confidence scoring',
-                duration: Date.now() - patternStart
-            });
-            // Cleanup test pattern
-            db.run(`DELETE FROM patterns WHERE id = ?`, [patternId]);
-        }
-        catch (e) {
-            tests.push({
-                name: 'Pattern storage',
-                passed: false,
-                details: e instanceof Error ? e.message : 'Pattern storage failed',
-                duration: Date.now() - patternStart
-            });
-        }
-        // Test 6: Vector index configuration
-        const indexStart = Date.now();
-        try {
-            const indexResult = db.exec(`SELECT name, dimensions, hnsw_m, hnsw_ef_construction FROM vector_indexes`);
-            const indexes = indexResult[0]?.values || [];
-            tests.push({
-                name: 'Vector index config',
-                passed: indexes.length > 0,
-                details: `${indexes.length} indexes configured (HNSW M=16, ef=200)`,
-                duration: Date.now() - indexStart
-            });
-        }
-        catch (e) {
-            tests.push({
-                name: 'Vector index config',
-                passed: false,
-                details: e instanceof Error ? e.message : 'Index check failed',
-                duration: Date.now() - indexStart
-            });
-        }
-        // Cleanup test entry
-        db.run(`DELETE FROM memory_entries WHERE id = ?`, [testId]);
-        // Save changes atomically
-        const data = db.export();
-        const dbTmpHealth = dbPath + '.tmp';
-        fs.writeFileSync(dbTmpHealth, Buffer.from(data));
-        fs.renameSync(dbTmpHealth, dbPath);
-        db.close();
-        const passed = tests.filter(t => t.passed).length;
-        const failed = tests.filter(t => !t.passed).length;
-        return {
-            success: failed === 0,
-            tests,
-            summary: {
-                passed,
-                failed,
-                total: tests.length
-            }
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            tests: [{
-                    name: 'Database access',
-                    passed: false,
-                    details: error instanceof Error ? error.message : 'Unknown error'
-                }],
-            summary: { passed: 0, failed: 1, total: 1 }
-        };
-    }
-}
-/**
- * Store an entry directly using sql.js
- * This bypasses MCP and writes directly to the database
- */
-export async function storeEntry(options) {
-    // ADR-053: Try AgentDB v1 bridge first
-    const bridge = await getBridge();
-    if (bridge) {
-        const bridgeResult = await bridge.bridgeStoreEntry(options);
-        if (bridgeResult)
-            return bridgeResult;
-    }
-    // Fallback: raw sql.js
-    const { key, value, namespace = 'default', generateEmbeddingFlag = true, tags = [], ttl, dbPath: customPath, upsert = false } = options;
-    const swarmDir = path.resolve(process.cwd(), '.swarm');
-    const dbPath = customPath ? path.resolve(customPath) : path.join(swarmDir, 'memory.db');
-    try {
-        if (!fs.existsSync(dbPath)) {
-            return { success: false, id: '', error: 'Database not initialized. Run: monomind memory init' };
-        }
-        // Ensure schema has all required columns (migration for older DBs)
-        await ensureSchemaColumns(dbPath);
-        const initSqlJs = (await import('sql.js')).default;
-        const SQL = await initSqlJs();
-        // Guard against excessively large DB files to prevent OOM.
-        const storeStat = fs.statSync(dbPath);
-        if (storeStat.size > MAX_DB_FILE_BYTES) {
-            return { success: false, id: '', error: `Database file too large: ${storeStat.size} bytes` };
-        }
-        const fileBuffer = fs.readFileSync(dbPath);
-        const db = new SQL.Database(fileBuffer);
-        const id = `entry_${Date.now()}_${Math.random().toString(36).substring(7)}`;
-        const now = Date.now();
-        // Generate embedding if requested
-        let embeddingJson = null;
-        let embeddingDimensions = null;
-        let embeddingModel = null;
-        if (generateEmbeddingFlag && value.length > 0) {
-            const embResult = await generateEmbedding(value);
-            embeddingJson = JSON.stringify(embResult.embedding);
-            embeddingDimensions = embResult.dimensions;
-            embeddingModel = embResult.model;
-        }
-        // Insert or update entry (upsert mode uses REPLACE)
-        const insertSql = upsert
-            ? `INSERT OR REPLACE INTO memory_entries (
-          id, key, namespace, content, type,
-          embedding, embedding_dimensions, embedding_model,
-          tags, metadata, created_at, updated_at, expires_at, status
-        ) VALUES (?, ?, ?, ?, 'semantic', ?, ?, ?, ?, ?, ?, ?, ?, 'active')`
-            : `INSERT INTO memory_entries (
-          id, key, namespace, content, type,
-          embedding, embedding_dimensions, embedding_model,
-          tags, metadata, created_at, updated_at, expires_at, status
-        ) VALUES (?, ?, ?, ?, 'semantic', ?, ?, ?, ?, ?, ?, ?, ?, 'active')`;
-        db.run(insertSql, [
-            id,
-            key,
-            namespace,
-            value,
-            embeddingJson,
-            embeddingDimensions,
-            embeddingModel,
-            tags.length > 0 ? JSON.stringify(tags) : null,
-            '{}',
-            now,
-            now,
-            ttl ? now + (ttl * 1000) : null
-        ]);
-        // Save atomically
-        const data = db.export();
-        const dbTmpStore = dbPath + '.tmp';
-        fs.writeFileSync(dbTmpStore, Buffer.from(data));
-        fs.renameSync(dbTmpStore, dbPath);
-        db.close();
-        // Add to HNSW index for faster future searches (validated to reject malformed embeddings)
-        if (embeddingJson) {
-            const embResult = safeParseEmbedding(embeddingJson);
-            if (embResult) {
-                await addToHNSWIndex(id, embResult, {
-                    id,
-                    key,
-                    namespace,
-                    content: value
-                });
-            }
-        }
-        return {
-            success: true,
-            id,
-            embedding: embeddingJson ? { dimensions: embeddingDimensions, model: embeddingModel } : undefined
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            id: '',
-            error: error instanceof Error ? error.message : String(error)
-        };
-    }
-}
-/**
- * Search entries using sql.js with vector similarity
- * Uses HNSW index for 150x faster search when available
- */
-export async function searchEntries(options) {
-    // ADR-053: Try AgentDB v1 bridge first
-    const bridge = await getBridge();
-    if (bridge) {
-        const bridgeResult = await bridge.bridgeSearchEntries(options);
-        if (bridgeResult)
-            return bridgeResult;
-    }
-    // Fallback: raw sql.js
-    const { query, namespace, limit = 10, threshold = 0.3, dbPath: customPath } = options;
-    const effectiveNamespace = namespace || 'all';
-    const swarmDir = path.resolve(process.cwd(), '.swarm');
-    const dbPath = customPath ? path.resolve(customPath) : path.join(swarmDir, 'memory.db');
-    const startTime = Date.now();
-    try {
-        if (!fs.existsSync(dbPath)) {
-            return { success: false, results: [], searchTime: 0, error: 'Database not found' };
-        }
-        // Ensure schema has all required columns (migration for older DBs)
-        await ensureSchemaColumns(dbPath);
-        // Guard against excessively large DB files to prevent OOM.
-        const searchStat = fs.statSync(dbPath);
-        if (searchStat.size > MAX_DB_FILE_BYTES) {
-            return { success: false, results: [], searchTime: 0, error: `Database file too large: ${searchStat.size} bytes` };
-        }
-        // Generate query embedding
-        const queryEmb = await generateEmbedding(query);
-        const queryEmbedding = queryEmb.embedding;
-        // Try HNSW search first (150x faster)
-        const hnswResults = await searchHNSWIndex(queryEmbedding, { k: limit, namespace: effectiveNamespace });
-        if (hnswResults && hnswResults.length > 0) {
-            // Filter by threshold
-            const filtered = hnswResults.filter(r => r.score >= threshold);
-            return {
-                success: true,
-                results: filtered,
-                searchTime: Date.now() - startTime
-            };
-        }
-        // Fall back to brute-force SQLite search
-        const initSqlJs = (await import('sql.js')).default;
-        const SQL = await initSqlJs();
-        // Guard against excessively large DB files to prevent OOM.
-        const searchFbStat = fs.statSync(dbPath);
-        if (searchFbStat.size > MAX_DB_FILE_BYTES) {
-            return { success: false, results: [], searchTime: Date.now() - startTime, error: `Database file too large: ${searchFbStat.size} bytes` };
-        }
-        const fileBuffer = fs.readFileSync(dbPath);
-        const db = new SQL.Database(fileBuffer);
-        // Get entries with embeddings
-        const searchStmt = db.prepare(effectiveNamespace !== 'all'
-            ? `SELECT id, key, namespace, content, embedding FROM memory_entries WHERE status = 'active' AND namespace = ? LIMIT 1000`
-            : `SELECT id, key, namespace, content, embedding FROM memory_entries WHERE status = 'active' LIMIT 1000`);
-        if (effectiveNamespace !== 'all') {
-            searchStmt.bind([effectiveNamespace]);
-        }
-        const searchRows = [];
-        while (searchStmt.step()) {
-            searchRows.push(searchStmt.get());
-        }
-        searchStmt.free();
-        const entries = searchRows.length > 0 ? [{ values: searchRows }] : [];
-        const results = [];
-        if (entries[0]?.values) {
-            for (const row of entries[0].values) {
-                const [id, key, ns, content, embeddingJson] = row;
-                let score = 0;
-                if (embeddingJson) {
-                    const embedding = safeParseEmbedding(embeddingJson);
-                    if (embedding && embedding.length === queryEmbedding.length) {
-                        score = cosineSim(queryEmbedding, embedding);
-                    }
-                }
-                // Fallback to keyword matching
-                if (score < threshold) {
-                    const lowerContent = (content || '').toLowerCase();
-                    const lowerQuery = query.toLowerCase();
-                    const words = lowerQuery.split(/\s+/).filter(w => w.length > 0);
-                    if (words.length > 0) {
-                        const matchCount = words.filter(w => lowerContent.includes(w)).length;
-                        const keywordScore = matchCount / words.length * 0.5;
-                        score = Math.max(score, keywordScore);
-                    }
-                }
-                if (score >= threshold) {
-                    results.push({
-                        id: id.substring(0, 12),
-                        key: key || id.substring(0, 15),
-                        content: (content || '').substring(0, 60) + ((content || '').length > 60 ? '...' : ''),
-                        score,
-                        namespace: ns || 'default'
-                    });
-                }
-            }
-        }
-        db.close();
-        // Sort by score
-        results.sort((a, b) => b.score - a.score);
-        return {
-            success: true,
-            results: results.slice(0, limit),
-            searchTime: Date.now() - startTime
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            results: [],
-            searchTime: Date.now() - startTime,
-            error: error instanceof Error ? error.message : String(error)
-        };
-    }
-}
-/**
- * Optimized cosine similarity
- * V8 JIT-friendly - avoids manual unrolling which can hurt performance
- * ~0.5μs per 384-dim vector comparison
- */
-function cosineSim(a, b) {
-    if (!a || !b || a.length === 0 || b.length === 0)
-        return 0;
-    const len = Math.min(a.length, b.length);
-    let dot = 0, normA = 0, normB = 0;
-    // Simple loop - V8 optimizes this well
-    for (let i = 0; i < len; i++) {
-        const ai = a[i], bi = b[i];
-        dot += ai * bi;
-        normA += ai * ai;
-        normB += bi * bi;
-    }
-    // Combined sqrt for slightly better performance
-    const mag = Math.sqrt(normA * normB);
-    return mag === 0 ? 0 : dot / mag;
-}
-/**
- * List all entries from the memory database
- */
-export async function listEntries(options) {
-    // ADR-053: Try AgentDB v1 bridge first
-    const bridge = await getBridge();
-    if (bridge) {
-        const bridgeResult = await bridge.bridgeListEntries(options);
-        if (bridgeResult)
-            return bridgeResult;
-    }
-    // Fallback: raw sql.js
-    const { namespace, limit = 20, offset = 0, dbPath: customPath } = options;
-    const swarmDir = path.join(process.cwd(), '.swarm');
-    const dbPath = customPath || path.join(swarmDir, 'memory.db');
-    try {
-        if (!fs.existsSync(dbPath)) {
-            return { success: false, entries: [], total: 0, error: 'Database not found' };
-        }
-        // Ensure schema has all required columns (migration for older DBs)
-        await ensureSchemaColumns(dbPath);
-        const initSqlJs = (await import('sql.js')).default;
-        const SQL = await initSqlJs();
-        // Guard against excessively large DB files to prevent OOM.
-        const listStat = fs.statSync(dbPath);
-        if (listStat.size > MAX_DB_FILE_BYTES) {
-            return { success: false, entries: [], total: 0, error: `Database file too large: ${listStat.size} bytes` };
-        }
-        const fileBuffer = fs.readFileSync(dbPath);
-        const db = new SQL.Database(fileBuffer);
-        // Get total count
-        const countStmt = namespace
-            ? db.prepare(`SELECT COUNT(*) as cnt FROM memory_entries WHERE status = 'active' AND namespace = ?`)
-            : db.prepare(`SELECT COUNT(*) as cnt FROM memory_entries WHERE status = 'active'`);
-        if (namespace) {
-            countStmt.bind([namespace]);
-        }
-        const countRows = [];
-        while (countStmt.step()) {
-            countRows.push(countStmt.get());
-        }
-        countStmt.free();
-        const countResult = countRows.length > 0 ? [{ values: countRows }] : [];
-        const total = countResult[0]?.values?.[0]?.[0] || 0;
-        // Get entries — cap limit to 10 000 to prevent full-table loads that OOM
-        // the sql.js in-memory database on large datasets.
-        const MAX_LIST_LIMIT = 10_000;
-        const rawLimit = parseInt(String(limit), 10);
-        const safeLimit = Number.isFinite(rawLimit) && rawLimit > 0 ? Math.min(rawLimit, MAX_LIST_LIMIT) : 100;
-        const rawOffset = parseInt(String(offset), 10);
-        const safeOffset = Number.isFinite(rawOffset) && rawOffset >= 0 ? rawOffset : 0;
-        const listStmt = namespace
-            ? db.prepare(`SELECT id, key, namespace, content, embedding, access_count, created_at, updated_at FROM memory_entries WHERE status = 'active' AND namespace = ? ORDER BY updated_at DESC LIMIT ? OFFSET ?`)
-            : db.prepare(`SELECT id, key, namespace, content, embedding, access_count, created_at, updated_at FROM memory_entries WHERE status = 'active' ORDER BY updated_at DESC LIMIT ? OFFSET ?`);
-        if (namespace) {
-            listStmt.bind([namespace, safeLimit, safeOffset]);
-        }
-        else {
-            listStmt.bind([safeLimit, safeOffset]);
-        }
-        const listRows = [];
-        while (listStmt.step()) {
-            listRows.push(listStmt.get());
-        }
-        listStmt.free();
-        const result = listRows.length > 0 ? [{ values: listRows }] : [];
-        const entries = [];
-        if (result[0]?.values) {
-            for (const row of result[0].values) {
-                const [id, key, ns, content, embedding, accessCount, createdAt, updatedAt] = row;
-                entries.push({
-                    id: String(id).substring(0, 20),
-                    key: key || String(id).substring(0, 15),
-                    namespace: ns || 'default',
-                    size: (content || '').length,
-                    accessCount: accessCount || 0,
-                    createdAt: createdAt || new Date().toISOString(),
-                    updatedAt: updatedAt || new Date().toISOString(),
-                    hasEmbedding: !!embedding && embedding.length > 10
-                });
-            }
-        }
-        db.close();
-        return { success: true, entries, total };
-    }
-    catch (error) {
-        return {
-            success: false,
-            entries: [],
-            total: 0,
-            error: error instanceof Error ? error.message : String(error)
-        };
-    }
-}
-/**
- * Get a specific entry from the memory database
- */
-export async function getEntry(options) {
-    // ADR-053: Try AgentDB v1 bridge first
-    const bridge = await getBridge();
-    if (bridge) {
-        const bridgeResult = await bridge.bridgeGetEntry(options);
-        if (bridgeResult)
-            return bridgeResult;
-    }
-    // Fallback: raw sql.js
-    const { key, namespace = 'default', dbPath: customPath } = options;
-    const swarmDir = path.join(process.cwd(), '.swarm');
-    const dbPath = customPath || path.join(swarmDir, 'memory.db');
-    try {
-        if (!fs.existsSync(dbPath)) {
-            return { success: false, found: false, error: 'Database not found' };
-        }
-        // Ensure schema has all required columns (migration for older DBs)
-        await ensureSchemaColumns(dbPath);
-        const initSqlJs = (await import('sql.js')).default;
-        const SQL = await initSqlJs();
-        // Guard against excessively large DB files to prevent OOM.
-        const getStat = fs.statSync(dbPath);
-        if (getStat.size > MAX_DB_FILE_BYTES) {
-            return { success: false, found: false, error: `Database file too large: ${getStat.size} bytes` };
-        }
-        const fileBuffer = fs.readFileSync(dbPath);
-        const db = new SQL.Database(fileBuffer);
-        // Find entry by key
-        const getStmt = db.prepare(`
-      SELECT id, key, namespace, content, embedding, access_count, created_at, updated_at, tags
-      FROM memory_entries
-      WHERE status = 'active'
-        AND key = ?
-        AND namespace = ?
-      LIMIT 1
-    `);
-        getStmt.bind([key, namespace]);
-        const getRows = [];
-        while (getStmt.step()) {
-            getRows.push(getStmt.get());
-        }
-        getStmt.free();
-        const result = getRows.length > 0 ? [{ values: getRows }] : [];
-        if (!result[0]?.values?.[0]) {
-            db.close();
-            return { success: true, found: false };
-        }
-        const [id, entryKey, ns, content, embedding, accessCount, createdAt, updatedAt, tagsJson] = result[0].values[0];
-        db.close();
-        let tags = [];
-        if (tagsJson) {
-            try {
-                tags = JSON.parse(tagsJson);
-            }
-            catch {
-                // Invalid JSON
-            }
-        }
-        return {
-            success: true,
-            found: true,
-            entry: {
-                id: String(id),
-                key: entryKey || String(id),
-                namespace: ns || 'default',
-                content: content || '',
-                accessCount: (accessCount || 0) + 1,
-                createdAt: createdAt || new Date().toISOString(),
-                updatedAt: updatedAt || new Date().toISOString(),
-                hasEmbedding: !!embedding && embedding.length > 10,
-                tags
-            }
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            found: false,
-            error: error instanceof Error ? error.message : String(error)
-        };
-    }
-}
-/**
- * Delete a memory entry by key and namespace
- * Issue #980: Properly supports namespaced entries
- */
-export async function deleteEntry(options) {
-    // ADR-053: Try AgentDB v1 bridge first
-    const bridge = await getBridge();
-    if (bridge) {
-        const bridgeResult = await bridge.bridgeDeleteEntry(options);
-        if (bridgeResult) {
-            // #1122: Bridge path must also invalidate the in-memory HNSW index.
-            // Without this, deleted vectors remain as ghost entries in search results.
-            if (bridgeResult.deleted && hnswIndex?.entries) {
-                // Remove the entry from the HNSW entries map by key+namespace composite
-                for (const [id, entry] of hnswIndex.entries) {
-                    if (entry?.key === options.key && (entry?.namespace ?? 'default') === (options.namespace ?? 'default')) {
-                        hnswIndex.entries.delete(id);
-                        break;
-                    }
-                }
-                saveHNSWMetadata();
-                rebuildSearchIndex();
-            }
-            return bridgeResult;
-        }
-    }
-    // Fallback: raw sql.js
-    const { key, namespace = 'default', dbPath: customPath } = options;
-    const swarmDir = path.join(process.cwd(), '.swarm');
-    const dbPath = customPath || path.join(swarmDir, 'memory.db');
-    try {
-        if (!fs.existsSync(dbPath)) {
-            return {
-                success: false,
-                deleted: false,
-                key,
-                namespace,
-                remainingEntries: 0,
-                error: 'Database not found'
-            };
-        }
-        // Ensure schema has all required columns (migration for older DBs)
-        await ensureSchemaColumns(dbPath);
-        const initSqlJs = (await import('sql.js')).default;
-        const SQL = await initSqlJs();
-        // Guard against excessively large DB files to prevent OOM.
-        const deleteStat = fs.statSync(dbPath);
-        if (deleteStat.size > MAX_DB_FILE_BYTES) {
-            return { success: false, deleted: false, key, namespace, remainingEntries: 0, error: `Database file too large: ${deleteStat.size} bytes` };
-        }
-        const fileBuffer = fs.readFileSync(dbPath);
-        const db = new SQL.Database(fileBuffer);
-        // Check if entry exists first
-        const checkStmt = db.prepare(`
-      SELECT id FROM memory_entries
-      WHERE status = 'active'
-        AND key = ?
-        AND namespace = ?
-      LIMIT 1
-    `);
-        checkStmt.bind([key, namespace]);
-        const checkRows = [];
-        while (checkStmt.step()) {
-            checkRows.push(checkStmt.get());
-        }
-        checkStmt.free();
-        const checkResult = checkRows.length > 0 ? [{ values: checkRows }] : [];
-        if (!checkResult[0]?.values?.[0]) {
-            // Get remaining count before closing
-            const countResult = db.exec(`SELECT COUNT(*) FROM memory_entries WHERE status = 'active'`);
-            const remainingEntries = countResult[0]?.values?.[0]?.[0] || 0;
-            db.close();
-            return {
-                success: true,
-                deleted: false,
-                key,
-                namespace,
-                remainingEntries,
-                error: `Key '${key}' not found in namespace '${namespace}'`
-            };
-        }
-        // Capture the entry ID for HNSW cleanup
-        const entryId = String(checkResult[0].values[0][0]);
-        // Delete the entry (soft delete by setting status to 'deleted')
-        // Also null out the embedding to clean up vector data from SQLite
-        db.run(`
-      UPDATE memory_entries
-      SET status = 'deleted',
-          embedding = NULL,
-          updated_at = strftime('%s', 'now') * 1000
-      WHERE key = ?
-        AND namespace = ?
-        AND status = 'active'
-    `, [key, namespace]);
-        // Get remaining count
-        const countResult = db.exec(`SELECT COUNT(*) FROM memory_entries WHERE status = 'active'`);
-        const remainingEntries = countResult[0]?.values?.[0]?.[0] || 0;
-        // Save updated database atomically
-        const data = db.export();
-        const dbTmpDelete = dbPath + '.tmp';
-        fs.writeFileSync(dbTmpDelete, Buffer.from(data));
-        fs.renameSync(dbTmpDelete, dbPath);
-        db.close();
-        // Clean up in-memory HNSW index so ghost vectors don't appear in searches.
-        // Remove the entry from the HNSW entries map and invalidate the index.
-        // The next search will rebuild the HNSW index from the remaining DB rows.
-        if (hnswIndex?.entries) {
-            hnswIndex.entries.delete(entryId);
-            saveHNSWMetadata();
-            // Invalidate the HNSW index so it rebuilds from DB on next search.
-            // We can't surgically remove a vector from the HNSW graph, so we
-            // clear the entire index; it will be lazily rebuilt from SQLite.
-            rebuildSearchIndex();
-        }
-        return {
-            success: true,
-            deleted: true,
-            key,
-            namespace,
-            remainingEntries
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            deleted: false,
-            key,
-            namespace,
-            remainingEntries: 0,
-            error: error instanceof Error ? error.message : String(error)
-        };
-    }
-}
 export default {
     initializeMemoryDatabase,
     checkMemoryInitialization,