refactor: Streamline flow execution and message handling in ProjectMCPServer
- Replaced `InputValueRequest` with `SimplifiedAPIRequest` for improved input management.
- Updated flow execution to utilize `simple_run_flow`, enhancing clarity and performance.
- Refined progress notification handling to ensure tasks are only created when necessary.
- Improved message collection from flow outputs, ensuring robust handling of both messages and results.
- Enhanced error handling during tool execution to provide clearer feedback on failures.