Add authentication, user management, and database migration features

- Implement OAuth 2.0 and PAT authentication methods
- Add user management, roles, and profile functionality
- Add database migrations and admin user scripts
- Update services for authentication and user settings
- Add protected routes and permission hooks
- Update documentation for authentication and database access

backend/scripts/run-migrations.ts

@@ -0,0 +1,27 @@
+/**
+ * Run Database Migrations
+ * 
+ * Standalone script to run database migrations manually.
+ * 
+ * Usage:
+ *   npm run migrate
+ *   or
+ *   tsx scripts/run-migrations.ts
+ */
+
+import { runMigrations } from '../src/services/database/migrations.js';
+import { logger } from '../src/services/logger.js';
+
+async function main() {
+  try {
+    console.log('Starting database migrations...');
+    await runMigrations();
+    console.log('✓ Database migrations completed successfully');
+    process.exit(0);
+  } catch (error) {
+    console.error('✗ Migration failed:', error);
+    process.exit(1);
+  }
+}
+
+main();