refactor: update import paths for database modules and remove legacy db.js and schema.js files

server/routes/agent.js

@@ -4,7 +4,7 @@ import path from 'path';
 import os from 'os';
 import { promises as fs } from 'fs';
 import crypto from 'crypto';
-import { userDb, apiKeysDb, githubTokensDb } from '../database/db.js';
+import { userDb, apiKeysDb, githubTokensDb } from '../modules/database/index.js';
 import { addProjectManually } from '../projects.js';
 import { queryClaudeSDK } from '../claude-sdk.js';
 import { spawnCursor } from '../cursor-cli.js';

server/routes/auth.js

@@ -1,9 +1,11 @@
 import express from 'express';
 import bcrypt from 'bcrypt';
-import { userDb, db } from '../database/db.js';
+import { userDb } from '../modules/database/index.js';
+import { getConnection } from '../modules/database/connection.js';
 import { generateToken, authenticateToken } from '../middleware/auth.js';
 
 const router = express.Router();
+const db = getConnection();
 
 // Check auth status and setup requirements
 router.get('/status', async (req, res) => {
@@ -132,4 +134,4 @@ router.post('/logout', authenticateToken, (req, res) => {
   res.json({ success: true, message: 'Logged out successfully' });
 });
 
-export default router;
+export default router;

server/routes/codex.js

@@ -1,6 +1,6 @@
 import express from 'express';
 import { deleteCodexSession } from '../projects.js';
-import { sessionsDb } from '../database/db.js';
+import { sessionsDb } from '../modules/database/index.js';
 
 const router = express.Router();
 

server/routes/gemini.js

@@ -1,6 +1,6 @@
 import express from 'express';
 import sessionManager from '../sessionManager.js';
-import { sessionsDb } from '../database/db.js';
+import { sessionsDb } from '../modules/database/index.js';
 
 const router = express.Router();
 

server/routes/projects.js

@@ -4,6 +4,7 @@ import path from 'path';
 import { spawn } from 'child_process';
 import os from 'os';
 import { addProjectManually } from '../projects.js';
+import { githubTokensDb } from '../modules/database/index.js';
 
 const router = express.Router();
 
@@ -311,21 +312,7 @@ router.post('/create-workspace', async (req, res) => {
  * Helper function to get GitHub token from database
  */
 async function getGithubTokenById(tokenId, userId) {
-  const { db } = await import('../database/db.js');
-
-  const credential = db.prepare(
-    'SELECT * FROM user_credentials WHERE id = ? AND user_id = ? AND credential_type = ? AND is_active = 1'
-  ).get(tokenId, userId, 'github_token');
-
-  // Return in the expected format (github_token field for compatibility)
-  if (credential) {
-    return {
-      ...credential,
-      github_token: credential.credential_value
-    };
-  }
-
-  return null;
+  return githubTokensDb.getGithubTokenById(userId, tokenId);
 }
 
 /**

server/routes/settings.js

@@ -1,5 +1,5 @@
 import express from 'express';
-import { apiKeysDb, credentialsDb, notificationPreferencesDb, pushSubscriptionsDb } from '../database/db.js';
+import { apiKeysDb, credentialsDb, notificationPreferencesDb, pushSubscriptionsDb } from '../modules/database/index.js';
 import { getPublicKey } from '../services/vapid-keys.js';
 import { createNotificationEvent, notifyUserIfEnabled } from '../services/notification-orchestrator.js';
 

server/routes/user.js

@@ -1,5 +1,5 @@
 import express from 'express';
-import { userDb } from '../database/db.js';
+import { userDb } from '../modules/database/index.js';
 import { authenticateToken } from '../middleware/auth.js';
 import { getSystemGitConfig } from '../utils/gitConfig.js';
 import { spawn } from 'child_process';