refactor: migrate from better-sqlite3 to bun:sqlite

- Updated build-hooks.js to remove better-sqlite3 dependency and use bun:sqlite.
- Modified smart-install.js to eliminate checks and installations related to better-sqlite3.
- Refactored Database.ts, SessionSearch.ts, SessionStore.ts, and migrations.ts to import and utilize bun:sqlite.
- Replaced exec and pragma calls with appropriate run methods for bun:sqlite compatibility.
- Removed unnecessary native module verification and installation logic for better-sqlite3.

ecosystem.config.cjs

@@ -13,7 +13,7 @@ module.exports = {
   apps: [
     {
       name: 'claude-mem-worker',
-      script: './plugin/scripts/worker-service.cjs',
+      script: 'bun ./plugin/scripts/worker-service.cjs',
       // Windows: prevent visible console windows
       windowsHide: true,
       // INTENTIONAL: Watch mode enables auto-restart on plugin updates

package.json

@@ -50,7 +50,6 @@
     "@anthropic-ai/claude-agent-sdk": "^0.1.62",
     "@modelcontextprotocol/sdk": "^1.20.1",
     "ansi-to-html": "^0.7.2",
-    "better-sqlite3": "^12.5.0",
     "express": "^4.18.2",
     "glob": "^11.0.3",
     "handlebars": "^4.7.8",
@@ -60,7 +59,6 @@
     "zod-to-json-schema": "^3.24.6"
   },
   "devDependencies": {
-    "@types/better-sqlite3": "^7.6.8",
     "@types/cors": "^2.8.19",
     "@types/express": "^4.17.21",
     "@types/node": "^20.0.0",

plugin/package.json

@@ -1,13 +1,12 @@
 {
   "name": "claude-mem-plugin",
-  "version": "7.0.9",
+  "version": "7.0.10",
   "private": true,
   "description": "Runtime dependencies for claude-mem bundled hooks",
   "type": "module",
-  "dependencies": {
+  "dependencies": {},
-    "better-sqlite3": "^12.5.0"
-  },
   "engines": {
-    "node": ">=18.0.0"
+    "node": ">=18.0.0",
+    "bun": ">=1.0.0"
   }
 }

plugin/scripts/smart-install.js

@@ -287,17 +287,6 @@ async function runNpmInstall() {
         encoding: 'utf-8',
       });
 
-      // Verify better-sqlite3 was installed
-      if (!existsSync(BETTER_SQLITE3_PATH)) {
-        throw new Error('better-sqlite3 installation verification failed');
-      }
-
-      // Verify native modules actually work
-      const nativeModulesWork = await verifyNativeModules();
-      if (!nativeModulesWork) {
-        throw new Error('Native modules failed to load after install');
-      }
-
       const packageVersion = getPackageVersion();
       const nodeVersion = getNodeVersion();
       setInstalledVersion(packageVersion, nodeVersion);

scripts/build-hooks.js

@@ -59,8 +59,7 @@ async function buildHooks() {
     console.log('✓ Output directories ready');
 
     // Generate plugin/package.json for cache directory dependency installation
-    // The bundled hooks use `external: ['better-sqlite3']` so dependencies must be
+    // Note: bun:sqlite is a Bun built-in, no external dependencies needed for SQLite
-    // installed at runtime. This package.json enables npm install in the cache directory.
     console.log('\n📦 Generating plugin package.json...');
     const pluginPackageJson = {
       name: 'claude-mem-plugin',
@@ -68,11 +67,10 @@ async function buildHooks() {
       private: true,
       description: 'Runtime dependencies for claude-mem bundled hooks',
       type: 'module',
-      dependencies: {
+      dependencies: {},
-        'better-sqlite3': packageJson.dependencies['better-sqlite3']
-      },
       engines: {
-        node: '>=18.0.0'
+        node: '>=18.0.0',
+        bun: '>=1.0.0'
       }
     };
     fs.writeFileSync('plugin/package.json', JSON.stringify(pluginPackageJson, null, 2) + '\n');
@@ -103,7 +101,7 @@ async function buildHooks() {
       outfile: `${hooksDir}/${WORKER_SERVICE.name}.cjs`,
       minify: true,
       logLevel: 'error', // Suppress warnings (import.meta warning is benign)
-      external: ['better-sqlite3'],
+      external: ['bun:sqlite'],
       define: {
         '__DEFAULT_PACKAGE_VERSION__': `"${version}"`
       },
@@ -128,7 +126,7 @@ async function buildHooks() {
       outfile: `${hooksDir}/${MCP_SERVER.name}.cjs`,
       minify: true,
       logLevel: 'error',
-      external: ['better-sqlite3'],
+      external: ['bun:sqlite'],
       define: {
         '__DEFAULT_PACKAGE_VERSION__': `"${version}"`
       },
@@ -153,7 +151,7 @@ async function buildHooks() {
       outfile: `${hooksDir}/${CONTEXT_GENERATOR.name}.cjs`,
       minify: true,
       logLevel: 'error',
-      external: ['better-sqlite3'],
+      external: ['bun:sqlite'],
       define: {
         '__DEFAULT_PACKAGE_VERSION__': `"${version}"`
       }
@@ -176,7 +174,7 @@ async function buildHooks() {
         format: 'esm',
         outfile,
         minify: true,
-        external: ['better-sqlite3'],
+        external: ['bun:sqlite'],
         define: {
           '__DEFAULT_PACKAGE_VERSION__': `"${version}"`
         },

scripts/smart-install.js

@@ -25,7 +25,6 @@ const MARKETPLACE_ROOT = join(homedir(), '.claude', 'plugins', 'marketplaces', '
 const PACKAGE_JSON_PATH = join(MARKETPLACE_ROOT, 'package.json');
 const VERSION_MARKER_PATH = join(MARKETPLACE_ROOT, '.install-version');
 const NODE_MODULES_PATH = join(MARKETPLACE_ROOT, 'node_modules');
-const BETTER_SQLITE3_PATH = join(NODE_MODULES_PATH, 'better-sqlite3');
 
 // Colors for output
 const colors = {
@@ -104,11 +103,6 @@ function needsInstall() {
     return true;
   }
 
-  // Check if better-sqlite3 is installed
-  if (!existsSync(BETTER_SQLITE3_PATH)) {
-    log('📦 better-sqlite3 missing - reinstalling', colors.cyan);
-    return true;
-  }
 
   // Check version marker
   const currentPackageVersion = getPackageVersion();
@@ -143,46 +137,6 @@ function needsInstall() {
   return false;
 }
 
-/**
- * Verify that better-sqlite3 native module loads correctly
- * This catches ABI mismatches and corrupted builds
- */
-async function verifyNativeModules() {
-  try {
-    log('🔍 Verifying native modules...', colors.dim);
-
-    // CRITICAL: Use createRequire() to resolve from MARKETPLACE_ROOT
-    // This script may run from cache but must load modules from marketplace's node_modules
-    const require = createRequire(join(MARKETPLACE_ROOT, 'package.json'));
-    const Database = require('better-sqlite3');
-
-    // Try to create a test in-memory database
-    const db = new Database(':memory:');
-
-    // Run a simple query to ensure it works
-    const result = db.prepare('SELECT 1 + 1 as result').get();
-
-    // Clean up
-    db.close();
-
-    if (result.result !== 2) {
-      throw new Error('SQLite math check failed');
-    }
-
-    log('✓ Native modules verified', colors.dim);
-    return true;
-
-  } catch (error) {
-    if (error.code === 'ERR_DLOPEN_FAILED') {
-      log('⚠️  Native module ABI mismatch detected', colors.yellow);
-      return false;
-    }
-
-    // Other errors are unexpected - log and fail
-    log(`❌ Native module verification failed: ${error.message}`, colors.red);
-    return false;
-  }
-}
 
 function getWindowsErrorHelp(errorOutput) {
   // Detect Python version at runtime
@@ -203,7 +157,7 @@ function getWindowsErrorHelp(errorOutput) {
     '║                    Windows Installation Help                        ║',
     '╚══════════════════════════════════════════════════════════════════════╝',
     '',
-    '📋 better-sqlite3 requires build tools to compile native modules.',
+    '',
     '',
     '🔧 Option 1: Install Visual Studio Build Tools (Recommended)',
     '   1. Download: https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2022',
@@ -232,9 +186,6 @@ function getWindowsErrorHelp(errorOutput) {
     help.push('❌ Permission denied - try running as Administrator');
   }
 
-  help.push('');
-  help.push('📖 Full documentation: https://github.com/WiseLibs/better-sqlite3/blob/master/docs/troubleshooting.md');
-  help.push('');
 
   return help.join('\n');
 }
@@ -266,10 +217,7 @@ async function runNpmInstall() {
         windowsHide: true,
       });
 
-      // Verify better-sqlite3 was installed
+  
-      if (!existsSync(BETTER_SQLITE3_PATH)) {
-        throw new Error('better-sqlite3 installation verification failed');
-      }
 
       // NEW: Verify native modules actually work
       const nativeModulesWork = await verifyNativeModules();
@@ -300,11 +248,6 @@ async function runNpmInstall() {
   log('❌ Installation failed after retrying!', colors.bright);
   log('', colors.reset);
 
-  // Provide Windows-specific help
-  if (isWindows && lastError && lastError.message && lastError.message.includes('better-sqlite3')) {
-    log(getWindowsErrorHelp(lastError.message), colors.yellow);
-  }
-
   // Show generic error info with troubleshooting steps
   if (lastError) {
     if (lastError.stderr) {

src/services/sqlite/Database.ts

@@ -1,4 +1,4 @@
-import { Database } from 'better-sqlite3';
+import { Database } from 'bun:sqlite';
 import { DATA_DIR, DB_PATH, ensureDir } from '../../shared/paths.js';
 
 export interface Migration {

src/services/sqlite/SessionSearch.ts

@@ -1,4 +1,4 @@
-import Database from 'better-sqlite3';
+import { Database } from 'bun:sqlite';
 import { TableNameRow } from '../../types/database.js';
 import { DATA_DIR, DB_PATH, ensureDir } from '../../shared/paths.js';
 import {
@@ -18,7 +18,7 @@ import {
  * Vector search is handled by ChromaDB - this class only supports filtering without query text
  */
 export class SessionSearch {
-  private db: Database.Database;
+  private db: Database;
 
   constructor(dbPath?: string) {
     if (!dbPath) {
@@ -26,7 +26,7 @@ export class SessionSearch {
       dbPath = DB_PATH;
     }
     this.db = new Database(dbPath);
-    this.db.pragma('journal_mode = WAL');
+    this.db.run('PRAGMA journal_mode = WAL');
 
     // Ensure FTS tables exist
     this.ensureFTSTables();
@@ -60,7 +60,7 @@ export class SessionSearch {
       console.error('[SessionSearch] Creating FTS5 tables...');
 
       // Create observations_fts virtual table
-      this.db.exec(`
+      this.db.run(`
         CREATE VIRTUAL TABLE IF NOT EXISTS observations_fts USING fts5(
           title,
           subtitle,
@@ -74,14 +74,14 @@ export class SessionSearch {
       `);
 
       // Populate with existing data
-      this.db.exec(`
+      this.db.run(`
         INSERT INTO observations_fts(rowid, title, subtitle, narrative, text, facts, concepts)
         SELECT id, title, subtitle, narrative, text, facts, concepts
         FROM observations;
       `);
 
       // Create triggers for observations
-      this.db.exec(`
+      this.db.run(`
         CREATE TRIGGER IF NOT EXISTS observations_ai AFTER INSERT ON observations BEGIN
           INSERT INTO observations_fts(rowid, title, subtitle, narrative, text, facts, concepts)
           VALUES (new.id, new.title, new.subtitle, new.narrative, new.text, new.facts, new.concepts);
@@ -101,7 +101,7 @@ export class SessionSearch {
       `);
 
       // Create session_summaries_fts virtual table
-      this.db.exec(`
+      this.db.run(`
         CREATE VIRTUAL TABLE IF NOT EXISTS session_summaries_fts USING fts5(
           request,
           investigated,
@@ -115,14 +115,14 @@ export class SessionSearch {
       `);
 
       // Populate with existing data
-      this.db.exec(`
+      this.db.run(`
         INSERT INTO session_summaries_fts(rowid, request, investigated, learned, completed, next_steps, notes)
         SELECT id, request, investigated, learned, completed, next_steps, notes
         FROM session_summaries;
       `);
 
       // Create triggers for session_summaries
-      this.db.exec(`
+      this.db.run(`
         CREATE TRIGGER IF NOT EXISTS session_summaries_ai AFTER INSERT ON session_summaries BEGIN
           INSERT INTO session_summaries_fts(rowid, request, investigated, learned, completed, next_steps, notes)
           VALUES (new.id, new.request, new.investigated, new.learned, new.completed, new.next_steps, new.notes);

src/services/sqlite/SessionStore.ts

@@ -1,4 +1,4 @@
-import Database from 'better-sqlite3';
+import { Database } from 'bun:sqlite';
 import { DATA_DIR, DB_PATH, ensureDir } from '../../shared/paths.js';
 import { logger } from '../../utils/logger.js';
 import {
@@ -18,16 +18,16 @@ import {
  * Provides simple, synchronous CRUD operations for session-based memory
  */
 export class SessionStore {
-  public db: Database.Database;
+  public db: Database;
 
   constructor() {
     ensureDir(DATA_DIR);
     this.db = new Database(DB_PATH);
 
     // Ensure optimized settings
-    this.db.pragma('journal_mode = WAL');
+    this.db.run('PRAGMA journal_mode = WAL');
-    this.db.pragma('synchronous = NORMAL');
+    this.db.run('PRAGMA synchronous = NORMAL');
-    this.db.pragma('foreign_keys = ON');
+    this.db.run('PRAGMA foreign_keys = ON');
 
     // Initialize schema if needed (fresh database)
     this.initializeSchema();
@@ -49,7 +49,7 @@ export class SessionStore {
   private initializeSchema(): void {
     try {
       // Create schema_versions table if it doesn't exist
-      this.db.exec(`
+      this.db.run(`
         CREATE TABLE IF NOT EXISTS schema_versions (
           id INTEGER PRIMARY KEY,
           version INTEGER UNIQUE NOT NULL,
@@ -67,7 +67,7 @@ export class SessionStore {
         console.error('[SessionStore] Initializing fresh database with migration004...');
 
         // Migration004: SDK agent architecture tables
-        this.db.exec(`
+        this.db.run(`
           CREATE TABLE IF NOT EXISTS sdk_sessions (
             id INTEGER PRIMARY KEY AUTOINCREMENT,
             claude_session_id TEXT UNIQUE NOT NULL,
@@ -146,11 +146,11 @@ export class SessionStore {
       if (applied) return;
 
       // Check if column exists
-      const tableInfo = this.db.pragma('table_info(sdk_sessions)') as TableColumnInfo[];
+      const tableInfo = this.db.query('PRAGMA table_info(sdk_sessions)').all() as TableColumnInfo[];
       const hasWorkerPort = tableInfo.some(col => col.name === 'worker_port');
 
       if (!hasWorkerPort) {
-        this.db.exec('ALTER TABLE sdk_sessions ADD COLUMN worker_port INTEGER');
+        this.db.run('ALTER TABLE sdk_sessions ADD COLUMN worker_port INTEGER');
         console.error('[SessionStore] Added worker_port column to sdk_sessions table');
       }
 
@@ -171,29 +171,29 @@ export class SessionStore {
       if (applied) return;
 
       // Check sdk_sessions for prompt_counter
-      const sessionsInfo = this.db.pragma('table_info(sdk_sessions)') as TableColumnInfo[];
+      const sessionsInfo = this.db.query('PRAGMA table_info(sdk_sessions)').all() as TableColumnInfo[];
       const hasPromptCounter = sessionsInfo.some(col => col.name === 'prompt_counter');
 
       if (!hasPromptCounter) {
-        this.db.exec('ALTER TABLE sdk_sessions ADD COLUMN prompt_counter INTEGER DEFAULT 0');
+        this.db.run('ALTER TABLE sdk_sessions ADD COLUMN prompt_counter INTEGER DEFAULT 0');
         console.error('[SessionStore] Added prompt_counter column to sdk_sessions table');
       }
 
       // Check observations for prompt_number
-      const observationsInfo = this.db.pragma('table_info(observations)') as TableColumnInfo[];
+      const observationsInfo = this.db.query('PRAGMA table_info(observations)').all() as TableColumnInfo[];
       const obsHasPromptNumber = observationsInfo.some(col => col.name === 'prompt_number');
 
       if (!obsHasPromptNumber) {
-        this.db.exec('ALTER TABLE observations ADD COLUMN prompt_number INTEGER');
+        this.db.run('ALTER TABLE observations ADD COLUMN prompt_number INTEGER');
         console.error('[SessionStore] Added prompt_number column to observations table');
       }
 
       // Check session_summaries for prompt_number
-      const summariesInfo = this.db.pragma('table_info(session_summaries)') as TableColumnInfo[];
+      const summariesInfo = this.db.query('PRAGMA table_info(session_summaries)').all() as TableColumnInfo[];
       const sumHasPromptNumber = summariesInfo.some(col => col.name === 'prompt_number');
 
       if (!sumHasPromptNumber) {
-        this.db.exec('ALTER TABLE session_summaries ADD COLUMN prompt_number INTEGER');
+        this.db.run('ALTER TABLE session_summaries ADD COLUMN prompt_number INTEGER');
         console.error('[SessionStore] Added prompt_number column to session_summaries table');
       }
 
@@ -214,7 +214,7 @@ export class SessionStore {
       if (applied) return;
 
       // Check if UNIQUE constraint exists
-      const summariesIndexes = this.db.pragma('index_list(session_summaries)') as IndexInfo[];
+      const summariesIndexes = this.db.query('PRAGMA index_list(session_summaries)').all() as IndexInfo[];
       const hasUniqueConstraint = summariesIndexes.some(idx => idx.unique === 1);
 
       if (!hasUniqueConstraint) {
@@ -226,11 +226,11 @@ export class SessionStore {
       console.error('[SessionStore] Removing UNIQUE constraint from session_summaries.sdk_session_id...');
 
       // Begin transaction
-      this.db.exec('BEGIN TRANSACTION');
+      this.db.run('BEGIN TRANSACTION');
 
       try {
         // Create new table without UNIQUE constraint
-        this.db.exec(`
+        this.db.run(`
           CREATE TABLE session_summaries_new (
             id INTEGER PRIMARY KEY AUTOINCREMENT,
             sdk_session_id TEXT NOT NULL,
@@ -251,7 +251,7 @@ export class SessionStore {
         `);
 
         // Copy data from old table
-        this.db.exec(`
+        this.db.run(`
           INSERT INTO session_summaries_new
           SELECT id, sdk_session_id, project, request, investigated, learned,
                  completed, next_steps, files_read, files_edited, notes,
@@ -260,20 +260,20 @@ export class SessionStore {
         `);
 
         // Drop old table
-        this.db.exec('DROP TABLE session_summaries');
+        this.db.run('DROP TABLE session_summaries');
 
         // Rename new table
-        this.db.exec('ALTER TABLE session_summaries_new RENAME TO session_summaries');
+        this.db.run('ALTER TABLE session_summaries_new RENAME TO session_summaries');
 
         // Recreate indexes
-        this.db.exec(`
+        this.db.run(`
           CREATE INDEX idx_session_summaries_sdk_session ON session_summaries(sdk_session_id);
           CREATE INDEX idx_session_summaries_project ON session_summaries(project);
           CREATE INDEX idx_session_summaries_created ON session_summaries(created_at_epoch DESC);
         `);
 
         // Commit transaction
-        this.db.exec('COMMIT');
+        this.db.run('COMMIT');
 
         // Record migration
         this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(7, new Date().toISOString());
@@ -281,7 +281,7 @@ export class SessionStore {
         console.error('[SessionStore] Successfully removed UNIQUE constraint from session_summaries.sdk_session_id');
       } catch (error: any) {
         // Rollback on error
-        this.db.exec('ROLLBACK');
+        this.db.run('ROLLBACK');
         throw error;
       }
     } catch (error: any) {
@@ -299,7 +299,7 @@ export class SessionStore {
       if (applied) return;
 
       // Check if new fields already exist
-      const tableInfo = this.db.pragma('table_info(observations)') as TableColumnInfo[];
+      const tableInfo = this.db.query('PRAGMA table_info(observations)').all() as TableColumnInfo[];
       const hasTitle = tableInfo.some(col => col.name === 'title');
 
       if (hasTitle) {
@@ -311,7 +311,7 @@ export class SessionStore {
       console.error('[SessionStore] Adding hierarchical fields to observations table...');
 
       // Add new columns
-      this.db.exec(`
+      this.db.run(`
         ALTER TABLE observations ADD COLUMN title TEXT;
         ALTER TABLE observations ADD COLUMN subtitle TEXT;
         ALTER TABLE observations ADD COLUMN facts TEXT;
@@ -341,7 +341,7 @@ export class SessionStore {
       if (applied) return;
 
       // Check if text column is already nullable
-      const tableInfo = this.db.pragma('table_info(observations)') as TableColumnInfo[];
+      const tableInfo = this.db.query('PRAGMA table_info(observations)').all() as TableColumnInfo[];
       const textColumn = tableInfo.find(col => col.name === 'text');
 
       if (!textColumn || textColumn.notnull === 0) {
@@ -353,11 +353,11 @@ export class SessionStore {
       console.error('[SessionStore] Making observations.text nullable...');
 
       // Begin transaction
-      this.db.exec('BEGIN TRANSACTION');
+      this.db.run('BEGIN TRANSACTION');
 
       try {
         // Create new table with text as nullable
-        this.db.exec(`
+        this.db.run(`
           CREATE TABLE observations_new (
             id INTEGER PRIMARY KEY AUTOINCREMENT,
             sdk_session_id TEXT NOT NULL,
@@ -379,7 +379,7 @@ export class SessionStore {
         `);
 
         // Copy data from old table (all existing columns)
-        this.db.exec(`
+        this.db.run(`
           INSERT INTO observations_new
           SELECT id, sdk_session_id, project, text, type, title, subtitle, facts,
                  narrative, concepts, files_read, files_modified, prompt_number,
@@ -388,13 +388,13 @@ export class SessionStore {
         `);
 
         // Drop old table
-        this.db.exec('DROP TABLE observations');
+        this.db.run('DROP TABLE observations');
 
         // Rename new table
-        this.db.exec('ALTER TABLE observations_new RENAME TO observations');
+        this.db.run('ALTER TABLE observations_new RENAME TO observations');
 
         // Recreate indexes
-        this.db.exec(`
+        this.db.run(`
           CREATE INDEX idx_observations_sdk_session ON observations(sdk_session_id);
           CREATE INDEX idx_observations_project ON observations(project);
           CREATE INDEX idx_observations_type ON observations(type);
@@ -402,7 +402,7 @@ export class SessionStore {
         `);
 
         // Commit transaction
-        this.db.exec('COMMIT');
+        this.db.run('COMMIT');
 
         // Record migration
         this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(9, new Date().toISOString());
@@ -410,7 +410,7 @@ export class SessionStore {
         console.error('[SessionStore] Successfully made observations.text nullable');
       } catch (error: any) {
         // Rollback on error
-        this.db.exec('ROLLBACK');
+        this.db.run('ROLLBACK');
         throw error;
       }
     } catch (error: any) {
@@ -428,7 +428,7 @@ export class SessionStore {
       if (applied) return;
 
       // Check if table already exists
-      const tableInfo = this.db.pragma('table_info(user_prompts)') as TableColumnInfo[];
+      const tableInfo = this.db.query('PRAGMA table_info(user_prompts)').all() as TableColumnInfo[];
       if (tableInfo.length > 0) {
         // Already migrated
         this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(10, new Date().toISOString());
@@ -438,11 +438,11 @@ export class SessionStore {
       console.error('[SessionStore] Creating user_prompts table with FTS5 support...');
 
       // Begin transaction
-      this.db.exec('BEGIN TRANSACTION');
+      this.db.run('BEGIN TRANSACTION');
 
       try {
         // Create main table (using claude_session_id since sdk_session_id is set asynchronously by worker)
-        this.db.exec(`
+        this.db.run(`
           CREATE TABLE user_prompts (
             id INTEGER PRIMARY KEY AUTOINCREMENT,
             claude_session_id TEXT NOT NULL,
@@ -460,7 +460,7 @@ export class SessionStore {
         `);
 
         // Create FTS5 virtual table
-        this.db.exec(`
+        this.db.run(`
           CREATE VIRTUAL TABLE user_prompts_fts USING fts5(
             prompt_text,
             content='user_prompts',
@@ -469,7 +469,7 @@ export class SessionStore {
         `);
 
         // Create triggers to sync FTS5
-        this.db.exec(`
+        this.db.run(`
           CREATE TRIGGER user_prompts_ai AFTER INSERT ON user_prompts BEGIN
             INSERT INTO user_prompts_fts(rowid, prompt_text)
             VALUES (new.id, new.prompt_text);
@@ -489,7 +489,7 @@ export class SessionStore {
         `);
 
         // Commit transaction
-        this.db.exec('COMMIT');
+        this.db.run('COMMIT');
 
         // Record migration
         this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(10, new Date().toISOString());
@@ -497,7 +497,7 @@ export class SessionStore {
         console.error('[SessionStore] Successfully created user_prompts table with FTS5 support');
       } catch (error: any) {
         // Rollback on error
-        this.db.exec('ROLLBACK');
+        this.db.run('ROLLBACK');
         throw error;
       }
     } catch (error: any) {
@@ -517,20 +517,20 @@ export class SessionStore {
       if (applied) return;
 
       // Check if discovery_tokens column exists in observations table
-      const observationsInfo = this.db.pragma('table_info(observations)') as TableColumnInfo[];
+      const observationsInfo = this.db.query('PRAGMA table_info(observations)').all() as TableColumnInfo[];
       const obsHasDiscoveryTokens = observationsInfo.some(col => col.name === 'discovery_tokens');
 
       if (!obsHasDiscoveryTokens) {
-        this.db.exec('ALTER TABLE observations ADD COLUMN discovery_tokens INTEGER DEFAULT 0');
+        this.db.run('ALTER TABLE observations ADD COLUMN discovery_tokens INTEGER DEFAULT 0');
         console.error('[SessionStore] Added discovery_tokens column to observations table');
       }
 
       // Check if discovery_tokens column exists in session_summaries table
-      const summariesInfo = this.db.pragma('table_info(session_summaries)') as TableColumnInfo[];
+      const summariesInfo = this.db.query('PRAGMA table_info(session_summaries)').all() as TableColumnInfo[];
       const sumHasDiscoveryTokens = summariesInfo.some(col => col.name === 'discovery_tokens');
 
       if (!sumHasDiscoveryTokens) {
-        this.db.exec('ALTER TABLE session_summaries ADD COLUMN discovery_tokens INTEGER DEFAULT 0');
+        this.db.run('ALTER TABLE session_summaries ADD COLUMN discovery_tokens INTEGER DEFAULT 0');
         console.error('[SessionStore] Added discovery_tokens column to session_summaries table');
       }
 

src/services/sqlite/migrations.ts

@@ -1,4 +1,4 @@
-import { Database } from 'better-sqlite3';
+import { Database } from 'bun:sqlite';
 import { Migration } from './Database.js';
 
 /**