@timmeck/brain 1.0.0 → 1.1.1

package/src/db/migrations/003_code_schema.ts

@@ -1,53 +1,53 @@
-import type Database from 'better-sqlite3';
-
-export function up(db: Database.Database): void {
-  db.exec(`
-    CREATE TABLE IF NOT EXISTS code_modules (
-      id INTEGER PRIMARY KEY AUTOINCREMENT,
-      project_id INTEGER NOT NULL,
-      name TEXT NOT NULL,
-      file_path TEXT NOT NULL,
-      language TEXT NOT NULL,
-      fingerprint TEXT NOT NULL,
-      description TEXT,
-      source_hash TEXT NOT NULL,
-      lines_of_code INTEGER NOT NULL DEFAULT 0,
-      complexity INTEGER,
-      reusability_score REAL NOT NULL DEFAULT 0.0,
-      created_at TEXT NOT NULL DEFAULT (datetime('now')),
-      updated_at TEXT NOT NULL DEFAULT (datetime('now')),
-      FOREIGN KEY (project_id) REFERENCES projects(id) ON DELETE CASCADE
-    );
-
-    CREATE TABLE IF NOT EXISTS module_usages (
-      id INTEGER PRIMARY KEY AUTOINCREMENT,
-      module_id INTEGER NOT NULL,
-      used_in_project_id INTEGER NOT NULL,
-      used_in_file TEXT NOT NULL,
-      usage_type TEXT NOT NULL DEFAULT 'import',
-      first_used TEXT NOT NULL DEFAULT (datetime('now')),
-      last_used TEXT NOT NULL DEFAULT (datetime('now')),
-      FOREIGN KEY (module_id) REFERENCES code_modules(id) ON DELETE CASCADE,
-      FOREIGN KEY (used_in_project_id) REFERENCES projects(id) ON DELETE CASCADE
-    );
-
-    CREATE TABLE IF NOT EXISTS module_similarities (
-      id INTEGER PRIMARY KEY AUTOINCREMENT,
-      module_a_id INTEGER NOT NULL,
-      module_b_id INTEGER NOT NULL,
-      similarity_score REAL NOT NULL,
-      computed_at TEXT NOT NULL DEFAULT (datetime('now')),
-      FOREIGN KEY (module_a_id) REFERENCES code_modules(id) ON DELETE CASCADE,
-      FOREIGN KEY (module_b_id) REFERENCES code_modules(id) ON DELETE CASCADE,
-      UNIQUE(module_a_id, module_b_id)
-    );
-
-    CREATE INDEX IF NOT EXISTS idx_code_modules_project ON code_modules(project_id);
-    CREATE INDEX IF NOT EXISTS idx_code_modules_fingerprint ON code_modules(fingerprint);
-    CREATE INDEX IF NOT EXISTS idx_code_modules_language ON code_modules(language);
-    CREATE INDEX IF NOT EXISTS idx_module_usages_module ON module_usages(module_id);
-    CREATE INDEX IF NOT EXISTS idx_module_usages_project ON module_usages(used_in_project_id);
-    CREATE INDEX IF NOT EXISTS idx_module_similarities_a ON module_similarities(module_a_id);
-    CREATE INDEX IF NOT EXISTS idx_module_similarities_b ON module_similarities(module_b_id);
-  `);
-}
+import type Database from 'better-sqlite3';
+
+export function up(db: Database.Database): void {
+  db.exec(`
+    CREATE TABLE IF NOT EXISTS code_modules (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      project_id INTEGER NOT NULL,
+      name TEXT NOT NULL,
+      file_path TEXT NOT NULL,
+      language TEXT NOT NULL,
+      fingerprint TEXT NOT NULL,
+      description TEXT,
+      source_hash TEXT NOT NULL,
+      lines_of_code INTEGER NOT NULL DEFAULT 0,
+      complexity INTEGER,
+      reusability_score REAL NOT NULL DEFAULT 0.0,
+      created_at TEXT NOT NULL DEFAULT (datetime('now')),
+      updated_at TEXT NOT NULL DEFAULT (datetime('now')),
+      FOREIGN KEY (project_id) REFERENCES projects(id) ON DELETE CASCADE
+    );
+
+    CREATE TABLE IF NOT EXISTS module_usages (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      module_id INTEGER NOT NULL,
+      used_in_project_id INTEGER NOT NULL,
+      used_in_file TEXT NOT NULL,
+      usage_type TEXT NOT NULL DEFAULT 'import',
+      first_used TEXT NOT NULL DEFAULT (datetime('now')),
+      last_used TEXT NOT NULL DEFAULT (datetime('now')),
+      FOREIGN KEY (module_id) REFERENCES code_modules(id) ON DELETE CASCADE,
+      FOREIGN KEY (used_in_project_id) REFERENCES projects(id) ON DELETE CASCADE
+    );
+
+    CREATE TABLE IF NOT EXISTS module_similarities (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      module_a_id INTEGER NOT NULL,
+      module_b_id INTEGER NOT NULL,
+      similarity_score REAL NOT NULL,
+      computed_at TEXT NOT NULL DEFAULT (datetime('now')),
+      FOREIGN KEY (module_a_id) REFERENCES code_modules(id) ON DELETE CASCADE,
+      FOREIGN KEY (module_b_id) REFERENCES code_modules(id) ON DELETE CASCADE,
+      UNIQUE(module_a_id, module_b_id)
+    );
+
+    CREATE INDEX IF NOT EXISTS idx_code_modules_project ON code_modules(project_id);
+    CREATE INDEX IF NOT EXISTS idx_code_modules_fingerprint ON code_modules(fingerprint);
+    CREATE INDEX IF NOT EXISTS idx_code_modules_language ON code_modules(language);
+    CREATE INDEX IF NOT EXISTS idx_module_usages_module ON module_usages(module_id);
+    CREATE INDEX IF NOT EXISTS idx_module_usages_project ON module_usages(used_in_project_id);
+    CREATE INDEX IF NOT EXISTS idx_module_similarities_a ON module_similarities(module_a_id);
+    CREATE INDEX IF NOT EXISTS idx_module_similarities_b ON module_similarities(module_b_id);
+  `);
+}

package/src/db/migrations/004_synapses_schema.ts

@@ -1,57 +1,57 @@
-import type Database from 'better-sqlite3';
-
-export function up(db: Database.Database): void {
-  db.exec(`
-    CREATE TABLE IF NOT EXISTS synapses (
-      id INTEGER PRIMARY KEY AUTOINCREMENT,
-      source_type TEXT NOT NULL,
-      source_id INTEGER NOT NULL,
-      target_type TEXT NOT NULL,
-      target_id INTEGER NOT NULL,
-      synapse_type TEXT NOT NULL,
-      weight REAL NOT NULL DEFAULT 0.5,
-      metadata TEXT,
-      created_at TEXT NOT NULL DEFAULT (datetime('now')),
-      updated_at TEXT NOT NULL DEFAULT (datetime('now')),
-      UNIQUE(source_type, source_id, target_type, target_id, synapse_type)
-    );
-
-    CREATE TABLE IF NOT EXISTS insights (
-      id INTEGER PRIMARY KEY AUTOINCREMENT,
-      type TEXT NOT NULL,
-      title TEXT NOT NULL,
-      description TEXT NOT NULL,
-      evidence TEXT NOT NULL DEFAULT '[]',
-      priority INTEGER NOT NULL DEFAULT 0,
-      project_id INTEGER,
-      active INTEGER NOT NULL DEFAULT 1,
-      expires_at TEXT,
-      created_at TEXT NOT NULL DEFAULT (datetime('now')),
-      FOREIGN KEY (project_id) REFERENCES projects(id) ON DELETE SET NULL
-    );
-
-    CREATE TABLE IF NOT EXISTS notifications (
-      id INTEGER PRIMARY KEY AUTOINCREMENT,
-      type TEXT NOT NULL,
-      title TEXT NOT NULL,
-      message TEXT NOT NULL,
-      priority INTEGER NOT NULL DEFAULT 0,
-      project_id INTEGER,
-      acknowledged INTEGER NOT NULL DEFAULT 0,
-      acknowledged_at TEXT,
-      created_at TEXT NOT NULL DEFAULT (datetime('now')),
-      FOREIGN KEY (project_id) REFERENCES projects(id) ON DELETE SET NULL
-    );
-
-    CREATE INDEX IF NOT EXISTS idx_synapses_source ON synapses(source_type, source_id);
-    CREATE INDEX IF NOT EXISTS idx_synapses_target ON synapses(target_type, target_id);
-    CREATE INDEX IF NOT EXISTS idx_synapses_type ON synapses(synapse_type);
-    CREATE INDEX IF NOT EXISTS idx_synapses_weight ON synapses(weight);
-    CREATE INDEX IF NOT EXISTS idx_insights_type ON insights(type);
-    CREATE INDEX IF NOT EXISTS idx_insights_project ON insights(project_id);
-    CREATE INDEX IF NOT EXISTS idx_insights_active ON insights(active);
-    CREATE INDEX IF NOT EXISTS idx_insights_priority ON insights(priority);
-    CREATE INDEX IF NOT EXISTS idx_notifications_acknowledged ON notifications(acknowledged);
-    CREATE INDEX IF NOT EXISTS idx_notifications_project ON notifications(project_id);
-  `);
-}
+import type Database from 'better-sqlite3';
+
+export function up(db: Database.Database): void {
+  db.exec(`
+    CREATE TABLE IF NOT EXISTS synapses (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      source_type TEXT NOT NULL,
+      source_id INTEGER NOT NULL,
+      target_type TEXT NOT NULL,
+      target_id INTEGER NOT NULL,
+      synapse_type TEXT NOT NULL,
+      weight REAL NOT NULL DEFAULT 0.5,
+      metadata TEXT,
+      created_at TEXT NOT NULL DEFAULT (datetime('now')),
+      updated_at TEXT NOT NULL DEFAULT (datetime('now')),
+      UNIQUE(source_type, source_id, target_type, target_id, synapse_type)
+    );
+
+    CREATE TABLE IF NOT EXISTS insights (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      type TEXT NOT NULL,
+      title TEXT NOT NULL,
+      description TEXT NOT NULL,
+      evidence TEXT NOT NULL DEFAULT '[]',
+      priority INTEGER NOT NULL DEFAULT 0,
+      project_id INTEGER,
+      active INTEGER NOT NULL DEFAULT 1,
+      expires_at TEXT,
+      created_at TEXT NOT NULL DEFAULT (datetime('now')),
+      FOREIGN KEY (project_id) REFERENCES projects(id) ON DELETE SET NULL
+    );
+
+    CREATE TABLE IF NOT EXISTS notifications (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      type TEXT NOT NULL,
+      title TEXT NOT NULL,
+      message TEXT NOT NULL,
+      priority INTEGER NOT NULL DEFAULT 0,
+      project_id INTEGER,
+      acknowledged INTEGER NOT NULL DEFAULT 0,
+      acknowledged_at TEXT,
+      created_at TEXT NOT NULL DEFAULT (datetime('now')),
+      FOREIGN KEY (project_id) REFERENCES projects(id) ON DELETE SET NULL
+    );
+
+    CREATE INDEX IF NOT EXISTS idx_synapses_source ON synapses(source_type, source_id);
+    CREATE INDEX IF NOT EXISTS idx_synapses_target ON synapses(target_type, target_id);
+    CREATE INDEX IF NOT EXISTS idx_synapses_type ON synapses(synapse_type);
+    CREATE INDEX IF NOT EXISTS idx_synapses_weight ON synapses(weight);
+    CREATE INDEX IF NOT EXISTS idx_insights_type ON insights(type);
+    CREATE INDEX IF NOT EXISTS idx_insights_project ON insights(project_id);
+    CREATE INDEX IF NOT EXISTS idx_insights_active ON insights(active);
+    CREATE INDEX IF NOT EXISTS idx_insights_priority ON insights(priority);
+    CREATE INDEX IF NOT EXISTS idx_notifications_acknowledged ON notifications(acknowledged);
+    CREATE INDEX IF NOT EXISTS idx_notifications_project ON notifications(project_id);
+  `);
+}

package/src/db/migrations/005_fts_indexes.ts

@@ -1,78 +1,78 @@
-import type Database from 'better-sqlite3';
-
-export function up(db: Database.Database): void {
-  db.exec(`
-    -- Full-text search for errors
-    CREATE VIRTUAL TABLE IF NOT EXISTS errors_fts USING fts5(
-      type, message, raw_output, context, file_path,
-      content='errors',
-      content_rowid='id'
-    );
-
-    -- Sync triggers for errors_fts
-    CREATE TRIGGER IF NOT EXISTS errors_ai AFTER INSERT ON errors BEGIN
-      INSERT INTO errors_fts(rowid, type, message, raw_output, context, file_path)
-      VALUES (new.id, new.type, new.message, new.raw_output, new.context, new.file_path);
-    END;
-
-    CREATE TRIGGER IF NOT EXISTS errors_ad AFTER DELETE ON errors BEGIN
-      INSERT INTO errors_fts(errors_fts, rowid, type, message, raw_output, context, file_path)
-      VALUES ('delete', old.id, old.type, old.message, old.raw_output, old.context, old.file_path);
-    END;
-
-    CREATE TRIGGER IF NOT EXISTS errors_au AFTER UPDATE ON errors BEGIN
-      INSERT INTO errors_fts(errors_fts, rowid, type, message, raw_output, context, file_path)
-      VALUES ('delete', old.id, old.type, old.message, old.raw_output, old.context, old.file_path);
-      INSERT INTO errors_fts(rowid, type, message, raw_output, context, file_path)
-      VALUES (new.id, new.type, new.message, new.raw_output, new.context, new.file_path);
-    END;
-
-    -- Full-text search for solutions
-    CREATE VIRTUAL TABLE IF NOT EXISTS solutions_fts USING fts5(
-      description, commands, code_change,
-      content='solutions',
-      content_rowid='id'
-    );
-
-    CREATE TRIGGER IF NOT EXISTS solutions_ai AFTER INSERT ON solutions BEGIN
-      INSERT INTO solutions_fts(rowid, description, commands, code_change)
-      VALUES (new.id, new.description, new.commands, new.code_change);
-    END;
-
-    CREATE TRIGGER IF NOT EXISTS solutions_ad AFTER DELETE ON solutions BEGIN
-      INSERT INTO solutions_fts(solutions_fts, rowid, description, commands, code_change)
-      VALUES ('delete', old.id, old.description, old.commands, old.code_change);
-    END;
-
-    CREATE TRIGGER IF NOT EXISTS solutions_au AFTER UPDATE ON solutions BEGIN
-      INSERT INTO solutions_fts(solutions_fts, rowid, description, commands, code_change)
-      VALUES ('delete', old.id, old.description, old.commands, old.code_change);
-      INSERT INTO solutions_fts(rowid, description, commands, code_change)
-      VALUES (new.id, new.description, new.commands, new.code_change);
-    END;
-
-    -- Full-text search for code modules
-    CREATE VIRTUAL TABLE IF NOT EXISTS code_modules_fts USING fts5(
-      name, file_path, description, language,
-      content='code_modules',
-      content_rowid='id'
-    );
-
-    CREATE TRIGGER IF NOT EXISTS code_modules_ai AFTER INSERT ON code_modules BEGIN
-      INSERT INTO code_modules_fts(rowid, name, file_path, description, language)
-      VALUES (new.id, new.name, new.file_path, new.description, new.language);
-    END;
-
-    CREATE TRIGGER IF NOT EXISTS code_modules_ad AFTER DELETE ON code_modules BEGIN
-      INSERT INTO code_modules_fts(code_modules_fts, rowid, name, file_path, description, language)
-      VALUES ('delete', old.id, old.name, old.file_path, old.description, old.language);
-    END;
-
-    CREATE TRIGGER IF NOT EXISTS code_modules_au AFTER UPDATE ON code_modules BEGIN
-      INSERT INTO code_modules_fts(code_modules_fts, rowid, name, file_path, description, language)
-      VALUES ('delete', old.id, old.name, old.file_path, old.description, old.language);
-      INSERT INTO code_modules_fts(rowid, name, file_path, description, language)
-      VALUES (new.id, new.name, new.file_path, new.description, new.language);
-    END;
-  `);
-}
+import type Database from 'better-sqlite3';
+
+export function up(db: Database.Database): void {
+  db.exec(`
+    -- Full-text search for errors
+    CREATE VIRTUAL TABLE IF NOT EXISTS errors_fts USING fts5(
+      type, message, raw_output, context, file_path,
+      content='errors',
+      content_rowid='id'
+    );
+
+    -- Sync triggers for errors_fts
+    CREATE TRIGGER IF NOT EXISTS errors_ai AFTER INSERT ON errors BEGIN
+      INSERT INTO errors_fts(rowid, type, message, raw_output, context, file_path)
+      VALUES (new.id, new.type, new.message, new.raw_output, new.context, new.file_path);
+    END;
+
+    CREATE TRIGGER IF NOT EXISTS errors_ad AFTER DELETE ON errors BEGIN
+      INSERT INTO errors_fts(errors_fts, rowid, type, message, raw_output, context, file_path)
+      VALUES ('delete', old.id, old.type, old.message, old.raw_output, old.context, old.file_path);
+    END;
+
+    CREATE TRIGGER IF NOT EXISTS errors_au AFTER UPDATE ON errors BEGIN
+      INSERT INTO errors_fts(errors_fts, rowid, type, message, raw_output, context, file_path)
+      VALUES ('delete', old.id, old.type, old.message, old.raw_output, old.context, old.file_path);
+      INSERT INTO errors_fts(rowid, type, message, raw_output, context, file_path)
+      VALUES (new.id, new.type, new.message, new.raw_output, new.context, new.file_path);
+    END;
+
+    -- Full-text search for solutions
+    CREATE VIRTUAL TABLE IF NOT EXISTS solutions_fts USING fts5(
+      description, commands, code_change,
+      content='solutions',
+      content_rowid='id'
+    );
+
+    CREATE TRIGGER IF NOT EXISTS solutions_ai AFTER INSERT ON solutions BEGIN
+      INSERT INTO solutions_fts(rowid, description, commands, code_change)
+      VALUES (new.id, new.description, new.commands, new.code_change);
+    END;
+
+    CREATE TRIGGER IF NOT EXISTS solutions_ad AFTER DELETE ON solutions BEGIN
+      INSERT INTO solutions_fts(solutions_fts, rowid, description, commands, code_change)
+      VALUES ('delete', old.id, old.description, old.commands, old.code_change);
+    END;
+
+    CREATE TRIGGER IF NOT EXISTS solutions_au AFTER UPDATE ON solutions BEGIN
+      INSERT INTO solutions_fts(solutions_fts, rowid, description, commands, code_change)
+      VALUES ('delete', old.id, old.description, old.commands, old.code_change);
+      INSERT INTO solutions_fts(rowid, description, commands, code_change)
+      VALUES (new.id, new.description, new.commands, new.code_change);
+    END;
+
+    -- Full-text search for code modules
+    CREATE VIRTUAL TABLE IF NOT EXISTS code_modules_fts USING fts5(
+      name, file_path, description, language,
+      content='code_modules',
+      content_rowid='id'
+    );
+
+    CREATE TRIGGER IF NOT EXISTS code_modules_ai AFTER INSERT ON code_modules BEGIN
+      INSERT INTO code_modules_fts(rowid, name, file_path, description, language)
+      VALUES (new.id, new.name, new.file_path, new.description, new.language);
+    END;
+
+    CREATE TRIGGER IF NOT EXISTS code_modules_ad AFTER DELETE ON code_modules BEGIN
+      INSERT INTO code_modules_fts(code_modules_fts, rowid, name, file_path, description, language)
+      VALUES ('delete', old.id, old.name, old.file_path, old.description, old.language);
+    END;
+
+    CREATE TRIGGER IF NOT EXISTS code_modules_au AFTER UPDATE ON code_modules BEGIN
+      INSERT INTO code_modules_fts(code_modules_fts, rowid, name, file_path, description, language)
+      VALUES ('delete', old.id, old.name, old.file_path, old.description, old.language);
+      INSERT INTO code_modules_fts(rowid, name, file_path, description, language)
+      VALUES (new.id, new.name, new.file_path, new.description, new.language);
+    END;
+  `);
+}

package/src/db/migrations/006_synapses_phase3.ts

@@ -1,17 +1,17 @@
-import type Database from 'better-sqlite3';
-
-export function up(db: Database.Database): void {
-  // Add activation_count and last_activated_at columns
-  const columns = db.pragma('table_info(synapses)') as Array<{ name: string }>;
-  const colNames = columns.map(c => c.name);
-
-  if (!colNames.includes('activation_count')) {
-    db.exec(`ALTER TABLE synapses ADD COLUMN activation_count INTEGER NOT NULL DEFAULT 1`);
-  }
-  if (!colNames.includes('last_activated_at')) {
-    db.exec(`ALTER TABLE synapses ADD COLUMN last_activated_at TEXT NOT NULL DEFAULT (datetime('now'))`);
-  }
-
-  // Add index for decay queries
-  db.exec(`CREATE INDEX IF NOT EXISTS idx_synapses_last_activated ON synapses(last_activated_at)`);
-}
+import type Database from 'better-sqlite3';
+
+export function up(db: Database.Database): void {
+  // Add activation_count and last_activated_at columns
+  const columns = db.pragma('table_info(synapses)') as Array<{ name: string }>;
+  const colNames = columns.map(c => c.name);
+
+  if (!colNames.includes('activation_count')) {
+    db.exec(`ALTER TABLE synapses ADD COLUMN activation_count INTEGER NOT NULL DEFAULT 1`);
+  }
+  if (!colNames.includes('last_activated_at')) {
+    db.exec(`ALTER TABLE synapses ADD COLUMN last_activated_at TEXT NOT NULL DEFAULT (datetime('now'))`);
+  }
+
+  // Add index for decay queries
+  db.exec(`CREATE INDEX IF NOT EXISTS idx_synapses_last_activated ON synapses(last_activated_at)`);
+}

package/src/db/migrations/index.ts

@@ -1,64 +1,64 @@
-import type Database from 'better-sqlite3';
-import { getLogger } from '../../utils/logger.js';
-import { up as coreSchema } from './001_core_schema.js';
-import { up as learningSchema } from './002_learning_schema.js';
-import { up as codeSchema } from './003_code_schema.js';
-import { up as synapsesSchema } from './004_synapses_schema.js';
-import { up as ftsIndexes } from './005_fts_indexes.js';
-import { up as synapsesPhase3 } from './006_synapses_phase3.js';
-
-interface Migration {
-  version: number;
-  name: string;
-  up: (db: Database.Database) => void;
-}
-
-const migrations: Migration[] = [
-  { version: 1, name: '001_core_schema', up: coreSchema },
-  { version: 2, name: '002_learning_schema', up: learningSchema },
-  { version: 3, name: '003_code_schema', up: codeSchema },
-  { version: 4, name: '004_synapses_schema', up: synapsesSchema },
-  { version: 5, name: '005_fts_indexes', up: ftsIndexes },
-  { version: 6, name: '006_synapses_phase3', up: synapsesPhase3 },
-];
-
-function ensureMigrationsTable(db: Database.Database): void {
-  db.exec(`
-    CREATE TABLE IF NOT EXISTS migrations (
-      version INTEGER PRIMARY KEY,
-      name TEXT NOT NULL,
-      applied_at TEXT NOT NULL DEFAULT (datetime('now'))
-    );
-  `);
-}
-
-function getCurrentVersion(db: Database.Database): number {
-  const row = db.prepare('SELECT MAX(version) as version FROM migrations').get() as { version: number | null } | undefined;
-  return row?.version ?? 0;
-}
-
-export function runMigrations(db: Database.Database): void {
-  const logger = getLogger();
-  ensureMigrationsTable(db);
-
-  const currentVersion = getCurrentVersion(db);
-  const pending = migrations.filter(m => m.version > currentVersion);
-
-  if (pending.length === 0) {
-    logger.info('Database is up to date');
-    return;
-  }
-
-  logger.info(`Running ${pending.length} migration(s) from version ${currentVersion}`);
-
-  const runAll = db.transaction(() => {
-    for (const migration of pending) {
-      logger.info(`Applying migration ${migration.name}`);
-      migration.up(db);
-      db.prepare('INSERT INTO migrations (version, name) VALUES (?, ?)').run(migration.version, migration.name);
-    }
-  });
-
-  runAll();
-  logger.info(`Migrations complete. Now at version ${pending[pending.length - 1]!.version}`);
-}
+import type Database from 'better-sqlite3';
+import { getLogger } from '../../utils/logger.js';
+import { up as coreSchema } from './001_core_schema.js';
+import { up as learningSchema } from './002_learning_schema.js';
+import { up as codeSchema } from './003_code_schema.js';
+import { up as synapsesSchema } from './004_synapses_schema.js';
+import { up as ftsIndexes } from './005_fts_indexes.js';
+import { up as synapsesPhase3 } from './006_synapses_phase3.js';
+
+interface Migration {
+  version: number;
+  name: string;
+  up: (db: Database.Database) => void;
+}
+
+const migrations: Migration[] = [
+  { version: 1, name: '001_core_schema', up: coreSchema },
+  { version: 2, name: '002_learning_schema', up: learningSchema },
+  { version: 3, name: '003_code_schema', up: codeSchema },
+  { version: 4, name: '004_synapses_schema', up: synapsesSchema },
+  { version: 5, name: '005_fts_indexes', up: ftsIndexes },
+  { version: 6, name: '006_synapses_phase3', up: synapsesPhase3 },
+];
+
+function ensureMigrationsTable(db: Database.Database): void {
+  db.exec(`
+    CREATE TABLE IF NOT EXISTS migrations (
+      version INTEGER PRIMARY KEY,
+      name TEXT NOT NULL,
+      applied_at TEXT NOT NULL DEFAULT (datetime('now'))
+    );
+  `);
+}
+
+function getCurrentVersion(db: Database.Database): number {
+  const row = db.prepare('SELECT MAX(version) as version FROM migrations').get() as { version: number | null } | undefined;
+  return row?.version ?? 0;
+}
+
+export function runMigrations(db: Database.Database): void {
+  const logger = getLogger();
+  ensureMigrationsTable(db);
+
+  const currentVersion = getCurrentVersion(db);
+  const pending = migrations.filter(m => m.version > currentVersion);
+
+  if (pending.length === 0) {
+    logger.info('Database is up to date');
+    return;
+  }
+
+  logger.info(`Running ${pending.length} migration(s) from version ${currentVersion}`);
+
+  const runAll = db.transaction(() => {
+    for (const migration of pending) {
+      logger.info(`Applying migration ${migration.name}`);
+      migration.up(db);
+      db.prepare('INSERT INTO migrations (version, name) VALUES (?, ?)').run(migration.version, migration.name);
+    }
+  });
+
+  runAll();
+  logger.info(`Migrations complete. Now at version ${pending[pending.length - 1]!.version}`);
+}