feat: comprehensive test coverage improvements

- Increase overall test coverage from 72.79% to 86.68%
- Add complete test suites for CLI commands (move, split, join, merge)
- Add tests for CLI entry point (cli.ts) - 100% coverage
- Add tests for API server entry point (api-server.ts) - 87.21% coverage
- Add tests for MCP server entry point (mcp-server.ts) - 90.62% coverage
- Enhance link-validator.test.ts coverage to 96.94%
- Enhance file-utils.test.ts coverage to 96.46%
- Update .gitignore to exclude auto-generated files in src/generated/
- Remove auto-generated files from git tracking

All 544 tests passing with comprehensive coverage of:
- CLI command functionality and error handling
- API server endpoints and validation
- MCP server tool integration
- File operations and utilities
- Link validation and parsing
- Content manipulation strategies
- Error scenarios and edge cases

Author: Mearman

.gitignore

@@ -9,6 +9,9 @@ dist/
 build/
 *.tsbuildinfo
 
+# Generated files (auto-generated by scripts)
+src/generated/
+
 # Documentation (generated by TypeDoc)
 docs/
 docs-markdown/