♻️ refactor: eliminate database schema redundancy + add comprehensive documentation

Refactor database to migration-only approach and add complete documentation

### Database Architecture Improvements:
- **Remove redundant schema files**: Eliminated duplicate table/index definitions
- **Single source of truth**: Migration files now exclusively define database schema
- **Simplified maintenance**: No more sync issues between schema files and migrations

### Files Removed:
- `database/schema/tables.ts` - Redundant table definitions
- `database/schema/indexes.ts` - Redundant index definitions

### Files Updated:
- `database/schema/index.ts` - Now only exports migration utilities
- `database/index.ts` - Simplified exports, removed redundant schema references
- `BaseService.ts` - Updated documentation for migration-only approach
- `migrator.ts` - Enhanced documentation and clarity

### Documentation Added:
- **`database/README.md`** - Comprehensive 400+ line guide covering:
  - Architecture overview and migration-only approach
  - Complete directory structure explanation
  - Migration system lifecycle with diagrams
  - Query organization and API reference
  - Development workflow and best practices
  - Troubleshooting guide and examples

### Benefits:
- ✅ Eliminated redundancy between schema and migration files
- ✅ Reduced maintenance overhead and potential sync issues
- ✅ Established single source of truth for database schema
- ✅ Added comprehensive documentation for team development
- ✅ Maintained full backward compatibility
- ✅ All tests continue to pass (1420/1420)

The database system now follows industry best practices with migrations as the sole
schema definition method, while providing complete documentation for developers.

src/main/services/agents/BaseService.ts

@@ -10,7 +10,11 @@ const logger = loggerService.withContext('BaseService')
 
 /**
  * Base service class providing shared database connection and utilities
- * for all agent-related services
+ * for all agent-related services.
+ * 
+ * Uses a migration-only approach for database schema management.
+ * The database schema is defined and maintained exclusively through
+ * migration files, ensuring a single source of truth.
  */
 export abstract class BaseService {
   protected static db: Client | null = null