refactor: modernize source code with improved structure and logging ...

- Add config.js for centralized configuration management
- Add logger.js for structured logging with levels
- Modernize main.js with JSDoc comments and error handling
- Enhance mcp-server.js with health check endpoint and logging
- Refactor db.js with validation and error handling functions
- Add TOOL_NAMES constant and improve mcp-tools.js documentation
- Refactor mcp-handlers.js with modular handler functions
- Enhance llama-client.js with timeout and input validation
- Update test to match new error messages
- All 35 tests passing with improved code quality