@claude-flow/cli 3.27.4 → 3.29.0

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

@@ -135,325 +135,325 @@ async function getBridge() {
  * Enhanced schema with pattern confidence, temporal decay, versioning
  * Vector embeddings enabled for semantic search
  */
-export const MEMORY_SCHEMA_V3 = `
--- RuFlo V3 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-v3', '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)
-);
-
--- ============================================
--- GRAPH EDGES (ADR-130 Phase 1)
--- Unified knowledge graph backend — sql.js canonical store
--- ============================================
-
--- Unified graph edges table (ADR-130)
--- Node IDs use domain-prefixed format: {domain}:{uuid}
--- where domain in (mem, agent, task, entity, span, pattern)
-CREATE TABLE IF NOT EXISTS graph_edges (
-  id              TEXT PRIMARY KEY,          -- edge-{uuid}
-  source_id       TEXT NOT NULL,             -- domain-prefixed node ID
-  target_id       TEXT NOT NULL,             -- domain-prefixed node ID
-  relation        TEXT NOT NULL,             -- e.g. "caused", "depends-on", "imports"
-  weight          REAL DEFAULT 1.0,
-  -- Temporal / reliability semantics (ADR-130 §"graph that forgets" property)
-  confidence      REAL DEFAULT 1.0,          -- [0,1]; updated by JUDGE step
-  decay_rate      REAL DEFAULT 0.0,          -- per-day exponential decay applied at read time
-  last_reinforced TEXT,                      -- ISO-8601; set when CONSOLIDATE re-touches edge
-  witness_id      TEXT,                      -- FK to verification/witness-fixes.json (ADR-103)
-  -- Embedding storage: "inline:{base64}" | "vector_indexes:{id}" | NULL
-  embedding_ref   TEXT,
-  metadata        TEXT,                      -- JSON blob for plugin-specific fields
-  created_at      TEXT NOT NULL
-);
-
-CREATE INDEX IF NOT EXISTS idx_graph_edges_source    ON graph_edges (source_id);
-CREATE INDEX IF NOT EXISTS idx_graph_edges_target    ON graph_edges (target_id);
-CREATE INDEX IF NOT EXISTS idx_graph_edges_relation  ON graph_edges (relation);
-CREATE INDEX IF NOT EXISTS idx_graph_edges_reinforced ON graph_edges (last_reinforced);
-
--- ============================================
--- SYSTEM METADATA
--- ============================================
-
-CREATE TABLE IF NOT EXISTS metadata (
-  key TEXT PRIMARY KEY,
-  value TEXT NOT NULL,
-  updated_at INTEGER DEFAULT (strftime('%s', 'now') * 1000)
-);
+export const MEMORY_SCHEMA_V3 = `
+-- RuFlo V3 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-v3', '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)
+);
+
+-- ============================================
+-- GRAPH EDGES (ADR-130 Phase 1)
+-- Unified knowledge graph backend — sql.js canonical store
+-- ============================================
+
+-- Unified graph edges table (ADR-130)
+-- Node IDs use domain-prefixed format: {domain}:{uuid}
+-- where domain in (mem, agent, task, entity, span, pattern)
+CREATE TABLE IF NOT EXISTS graph_edges (
+  id              TEXT PRIMARY KEY,          -- edge-{uuid}
+  source_id       TEXT NOT NULL,             -- domain-prefixed node ID
+  target_id       TEXT NOT NULL,             -- domain-prefixed node ID
+  relation        TEXT NOT NULL,             -- e.g. "caused", "depends-on", "imports"
+  weight          REAL DEFAULT 1.0,
+  -- Temporal / reliability semantics (ADR-130 §"graph that forgets" property)
+  confidence      REAL DEFAULT 1.0,          -- [0,1]; updated by JUDGE step
+  decay_rate      REAL DEFAULT 0.0,          -- per-day exponential decay applied at read time
+  last_reinforced TEXT,                      -- ISO-8601; set when CONSOLIDATE re-touches edge
+  witness_id      TEXT,                      -- FK to verification/witness-fixes.json (ADR-103)
+  -- Embedding storage: "inline:{base64}" | "vector_indexes:{id}" | NULL
+  embedding_ref   TEXT,
+  metadata        TEXT,                      -- JSON blob for plugin-specific fields
+  created_at      TEXT NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS idx_graph_edges_source    ON graph_edges (source_id);
+CREATE INDEX IF NOT EXISTS idx_graph_edges_target    ON graph_edges (target_id);
+CREATE INDEX IF NOT EXISTS idx_graph_edges_relation  ON graph_edges (relation);
+CREATE INDEX IF NOT EXISTS idx_graph_edges_reinforced ON graph_edges (last_reinforced);
+
+-- ============================================
+-- 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;
@@ -541,11 +541,11 @@ export async function getHNSWIndex(options) {
                 const fileBuffer = readFileMaybeEncrypted(dbPath, null);
                 const sqlDb = new SQL.Database(fileBuffer);
                 // Load all entries with embeddings
-                const result = sqlDb.exec(`
-          SELECT id, key, namespace, content, embedding
-          FROM memory_entries
-          WHERE status = 'active' AND embedding IS NOT NULL
-          LIMIT 10000
+                const result = sqlDb.exec(`
+          SELECT id, key, namespace, content, embedding
+          FROM memory_entries
+          WHERE status = 'active' AND embedding IS NOT NULL
+          LIMIT 10000
         `);
                 if (result[0]?.values) {
                     for (const row of result[0].values) {
@@ -939,24 +939,24 @@ export function flashAttentionSearch(query, vectors, options = {}) {
  * Initial metadata to insert after schema creation
  */
 export function getInitialMetadata(backend) {
-    return `
-INSERT OR REPLACE INTO metadata (key, value) VALUES
-  ('schema_version', '3.0.0'),
-  ('backend', '${backend}'),
-  ('created_at', '${new Date().toISOString()}'),
-  ('sql_js', 'true'),
-  ('vector_embeddings', 'enabled'),
-  ('pattern_learning', 'enabled'),
-  ('temporal_decay', 'enabled'),
-  ('hnsw_indexing', 'enabled');
-
--- Create default vector index configuration. Dimension matches the default
--- ONNX embedding model (Xenova/all-MiniLM-L6-v2, 384-dim); HNSW rejects
--- inserts whose dim does not match this row, so a 768 here breaks every
--- memory_store --vector and memory_search on a fresh install (#1947).
-INSERT OR IGNORE INTO vector_indexes (id, name, dimensions) VALUES
-  ('default', 'default', 384),
-  ('patterns', 'patterns', 384);
+    return `
+INSERT OR REPLACE INTO metadata (key, value) VALUES
+  ('schema_version', '3.0.0'),
+  ('backend', '${backend}'),
+  ('created_at', '${new Date().toISOString()}'),
+  ('sql_js', 'true'),
+  ('vector_embeddings', 'enabled'),
+  ('pattern_learning', 'enabled'),
+  ('temporal_decay', 'enabled'),
+  ('hnsw_indexing', 'enabled');
+
+-- Create default vector index configuration. Dimension matches the default
+-- ONNX embedding model (Xenova/all-MiniLM-L6-v2, 384-dim); HNSW rejects
+-- inserts whose dim does not match this row, so a 768 here breaks every
+-- memory_store --vector and memory_search on a fresh install (#1947).
+INSERT OR IGNORE INTO vector_indexes (id, name, dimensions) VALUES
+  ('default', 'default', 384),
+  ('patterns', 'patterns', 384);
 `;
 }
 /**
@@ -1409,20 +1409,20 @@ export async function repairVectorIndexes(dbPath, opts = {}) {
             return res;
         }
         if (!hasVectorIndexes) {
-            db.exec(`CREATE TABLE IF NOT EXISTS vector_indexes (
-        id TEXT PRIMARY KEY,
-        name TEXT NOT NULL UNIQUE,
-        dimensions INTEGER NOT NULL,
-        metric TEXT DEFAULT 'cosine' CHECK(metric IN ('cosine', 'euclidean', 'dot')),
-        hnsw_m INTEGER DEFAULT 16,
-        hnsw_ef_construction INTEGER DEFAULT 200,
-        hnsw_ef_search INTEGER DEFAULT 100,
-        quantization_type TEXT CHECK(quantization_type IN ('none', 'scalar', 'product')),
-        quantization_bits INTEGER DEFAULT 8,
-        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)
+            db.exec(`CREATE TABLE IF NOT EXISTS vector_indexes (
+        id TEXT PRIMARY KEY,
+        name TEXT NOT NULL UNIQUE,
+        dimensions INTEGER NOT NULL,
+        metric TEXT DEFAULT 'cosine' CHECK(metric IN ('cosine', 'euclidean', 'dot')),
+        hnsw_m INTEGER DEFAULT 16,
+        hnsw_ef_construction INTEGER DEFAULT 200,
+        hnsw_ef_search INTEGER DEFAULT 100,
+        quantization_type TEXT CHECK(quantization_type IN ('none', 'scalar', 'product')),
+        quantization_bits INTEGER DEFAULT 8,
+        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)
       )`);
             res.tableCreated = true;
         }
@@ -1717,14 +1717,14 @@ export async function applyTemporalDecay(dbPath) {
         const db = new SQL.Database(fileBuffer);
         // Apply decay: confidence *= exp(-decay_rate * days_since_last_use)
         const now = Date.now();
-        const decayQuery = `
-      UPDATE patterns
-      SET
-        confidence = confidence * (1.0 - decay_rate * ((? - COALESCE(last_matched_at, created_at)) / 86400000.0)),
-        updated_at = ?
-      WHERE status = 'active'
-        AND confidence > 0.1
-        AND (? - COALESCE(last_matched_at, created_at)) > 86400000
+        const decayQuery = `
+      UPDATE patterns
+      SET
+        confidence = confidence * (1.0 - decay_rate * ((? - COALESCE(last_matched_at, created_at)) / 86400000.0)),
+        updated_at = ?
+      WHERE status = 'active'
+        AND confidence > 0.1
+        AND (? - COALESCE(last_matched_at, created_at)) > 86400000
     `;
         db.run(decayQuery, [now, now, now]);
         const changes = db.getRowsModified();
@@ -2134,9 +2134,9 @@ export async function verifyMemoryInit(dbPath, options) {
         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', ?, ?)
+            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',
@@ -2178,10 +2178,10 @@ export async function verifyMemoryInit(dbPath, options) {
         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 = ?
+            db.run(`
+        UPDATE memory_entries
+        SET embedding = ?, embedding_dimensions = ?, embedding_model = ?
+        WHERE id = ?
       `, [embeddingJson, dimensions, model, testId]);
             tests.push({
                 name: 'Generate embedding',
@@ -2202,9 +2202,9 @@ export async function verifyMemoryInit(dbPath, options) {
         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, ?, ?)
+            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',
@@ -2333,15 +2333,15 @@ export async function storeEntry(options) {
         catch { /* vector_indexes may not exist on legacy DBs — fall through */ }
         // 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
+            ? `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
+            : `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,
@@ -2679,13 +2679,13 @@ export async function getEntry(options) {
         const fileBuffer = readFileMaybeEncrypted(dbPath, null);
         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
+        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 = [];
@@ -2700,10 +2700,10 @@ export async function getEntry(options) {
         }
         const [id, entryKey, ns, content, embedding, accessCount, createdAt, updatedAt, tagsJson] = result[0].values[0];
         // Update access count
-        db.run(`
-      UPDATE memory_entries
-      SET access_count = access_count + 1, last_accessed_at = strftime('%s', 'now') * 1000
-      WHERE id = ?
+        db.run(`
+      UPDATE memory_entries
+      SET access_count = access_count + 1, last_accessed_at = strftime('%s', 'now') * 1000
+      WHERE id = ?
     `, [String(id)]);
         // Save updated database
         const data = db.export();
@@ -2790,12 +2790,12 @@ export async function deleteEntry(options) {
         const fileBuffer = readFileMaybeEncrypted(dbPath, null);
         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
+        const checkStmt = db.prepare(`
+      SELECT id FROM memory_entries
+      WHERE status = 'active'
+        AND key = ?
+        AND namespace = ?
+      LIMIT 1
     `);
         checkStmt.bind([key, namespace]);
         const checkRows = [];
@@ -2822,14 +2822,14 @@ export async function deleteEntry(options) {
         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'
+        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'`);
@@ -2868,6 +2868,136 @@ export async function deleteEntry(options) {
         };
     }
 }
+// #2666 — Namespace reconciliation ("reaping"). `deleteEntry` above only ever
+// soft-deletes (UPDATE ... SET status='deleted'), and the row's (namespace,
+// key) stays occupied against the UNIQUE(namespace, key) constraint — a
+// caller that needs a namespace to be genuinely empty (e.g. a plugin
+// rebuilding its whole index after a source file was deleted, so a stale
+// row would otherwise survive forever with no dangling-ref/cycle signal to
+// ever catch it) has no way to get there through the public CLI/MCP surface.
+// `purgeNamespace` is a real `DELETE FROM memory_entries WHERE namespace = ?`
+// — irreversible, namespace-scoped, and lock-protected against a second
+// concurrent purge/delete on the same db file (see withMemoryDbLock below).
+//
+// This does NOT fully close #2621 (a concurrent daemon/MCP server already
+// mid read-modify-write on the sql.js fallback path can still flush an
+// older in-memory image after this purge commits, resurrecting rows) — that
+// requires every memory.db writer to respect the same lock, which is a
+// larger change than this namespace-reconcile primitive. The lock here
+// bounds the race to "another purge/delete running at the same instant",
+// which is the concrete case this feature needs to be safe against.
+const MEMORY_DB_LOCK_STALE_MS = 10_000;
+function delayMs(ms) {
+    return new Promise((r) => setTimeout(r, ms));
+}
+/**
+ * Advisory O_EXCL lock scoped to a single memory.db file (`<dbPath>.lock`),
+ * same stale-takeover pattern as services/global-ai-budget.ts. Only
+ * meaningful between callers that opt into it (purgeNamespace does); it
+ * cannot coordinate against writers that don't call this helper.
+ */
+export async function withMemoryDbLock(dbPath, fn) {
+    const lockFile = `${dbPath}.lock`;
+    const deadline = Date.now() + 5000;
+    for (;;) {
+        try {
+            const fd = fs.openSync(lockFile, fs.constants.O_CREAT | fs.constants.O_EXCL | fs.constants.O_WRONLY, 0o600);
+            fs.writeSync(fd, String(process.pid));
+            fs.closeSync(fd);
+            try {
+                return await fn();
+            }
+            finally {
+                try {
+                    fs.unlinkSync(lockFile);
+                }
+                catch { /* already gone */ }
+            }
+        }
+        catch (e) {
+            if (e.code !== 'EEXIST')
+                throw e;
+            try {
+                const st = fs.lstatSync(lockFile);
+                if (Date.now() - st.mtimeMs > MEMORY_DB_LOCK_STALE_MS) {
+                    fs.unlinkSync(lockFile);
+                    continue;
+                }
+            }
+            catch { /* raced — retry */ }
+            if (Date.now() > deadline) {
+                throw new Error(`timed out acquiring memory.db lock: ${lockFile}`);
+            }
+            await delayMs(25);
+        }
+    }
+}
+const NAMESPACE_PATTERN = /^[A-Za-z0-9._-]{1,128}$/;
+export async function purgeNamespace(options) {
+    const { namespace, dbPath: customPath } = options;
+    if (!NAMESPACE_PATTERN.test(namespace)) {
+        return { success: false, deletedCount: 0, remainingEntries: 0, error: `Invalid namespace: ${namespace}` };
+    }
+    const swarmDir = getMemoryRoot();
+    const dbPath = customPath ? path.resolve(customPath) : path.join(swarmDir, 'memory.db');
+    return withMemoryDbLock(dbPath, async () => {
+        // ADR-053: try the AgentDB v3 bridge first — a real SQLite handle, so
+        // the DELETE is a genuine transactional statement, not a whole-file
+        // read/mutate/rewrite.
+        const bridge = await getBridge();
+        if (bridge) {
+            const bridgeResult = await bridge.bridgePurgeNamespace({ namespace, dbPath });
+            if (bridgeResult) {
+                if (bridgeResult.deletedCount > 0 && hnswIndex?.entries) {
+                    for (const [id, entry] of hnswIndex.entries) {
+                        if ((entry?.namespace ?? 'default') === namespace)
+                            hnswIndex.entries.delete(id);
+                    }
+                    saveHNSWMetadata();
+                    rebuildSearchIndex();
+                }
+                return bridgeResult;
+            }
+        }
+        // Fallback: raw sql.js, same whole-file read/mutate/rewrite shape as
+        // deleteEntry's fallback path above (and the same encryption handling).
+        try {
+            if (!fs.existsSync(dbPath)) {
+                return { success: false, deletedCount: 0, remainingEntries: 0, error: 'Database not found' };
+            }
+            await ensureSchemaColumns(dbPath);
+            const initSqlJs = (await import('sql.js')).default;
+            const SQL = await initSqlJs();
+            const fileBuffer = readFileMaybeEncrypted(dbPath, null);
+            const db = new SQL.Database(fileBuffer);
+            const beforeResult = db.exec(`SELECT COUNT(*) FROM memory_entries WHERE namespace = ?`, [namespace]);
+            const deletedCount = beforeResult[0]?.values?.[0]?.[0] || 0;
+            db.run(`DELETE FROM memory_entries WHERE namespace = ?`, [namespace]);
+            const countResult = db.exec(`SELECT COUNT(*) FROM memory_entries WHERE status = 'active'`);
+            const remainingEntries = countResult[0]?.values?.[0]?.[0] || 0;
+            const data = db.export();
+            writeFileRestricted(dbPath, Buffer.from(data), { encrypt: true });
+            db.close();
+            if (deletedCount > 0 && hnswIndex?.entries) {
+                for (const [id, entry] of hnswIndex.entries) {
+                    if ((entry?.namespace ?? 'default') === namespace)
+                        hnswIndex.entries.delete(id);
+                }
+                saveHNSWMetadata();
+                rebuildSearchIndex();
+            }
+            return { success: true, deletedCount, remainingEntries };
+        }
+        catch (error) {
+            return {
+                success: false,
+                deletedCount: 0,
+                remainingEntries: 0,
+                error: error instanceof Error ? error.message : String(error),
+            };
+        }
+    });
+}
 export default {
     initializeMemoryDatabase,
     checkMemoryInitialization,
@@ -2882,6 +3012,8 @@ export default {
     listEntries,
     getEntry,
     deleteEntry,
+    purgeNamespace,
+    withMemoryDbLock,
     rebuildSearchIndex,
     MEMORY_SCHEMA_V3,
     getInitialMetadata