Comprehensive Refactor and Modernization

This release represents a major refactoring of the project, introducing a modern and more robust foundation for the Doxygen MCP Server. The changes focus on improving code quality, enhancing security, and standardizing the project's structure to align with best practices in the Python ecosystem.

Key Changes:

• Project Modernization: The repository has been migrated to use pyproject.toml for dependency management, replacing the legacy requirements.txt file. This provides a more standardized and declarative way to manage the project's build and dependencies.
• Code Quality & Security: The core server code in server.py was refactored to simplify implementation by utilizing the FastMCP class. Security was enhanced by adding sanitization to subprocess.run calls to mitigate potential command injection vulnerabilities.
• Standardized Documentation: The project's documentation has been reorganized for improved clarity and consistency. Files like BUGS.md, TROUBLESHOOTING.md, DEVELOPMENT.md, and LICENSE.md were renamed or created to follow standard conventions and provide a centralized location for contributor information.
• Testing and Environment: Installation and usage instructions were updated to use uv and uvenv, providing a modern and efficient way for users and clients to manage the project environment.