Add server integration tests, refactor initialization logic, and update coverage thresholds

- Replace health endpoint test with comprehensive server integration tests, including API routes, error handling, and environment configuration.
- Refactor `notes-api-server.js` to modularize initialization, repository creation, and server startup logic.
- Add graceful shutdown handling and exported helper methods for repositories.
- Update Jest coverage thresholds to reflect increased test coverage.

Author: starichkov