Refactor GPUMDkit with AI

[zhyan0603]

This pull request introduces major improvements to the documentation and contributing guidelines for GPUMDkit, clarifying project structure, coding conventions, and user guidance. It adds a new agent documentation file, updates the README with current links and versioning, and significantly expands the CONTRIBUTING.md with more detailed instructions and conventions for both shell and Python development. The changes also improve clarity around adding new features, handling command-line flags, and updating tutorials.

Documentation and User Guidance:

• Added a comprehensive AGENTS.md describing GPUMDkit's features, agent skills, and strict coding conventions for contributors.
• Updated README.md with new documentation links, version number bump to 1.5.6, improved help output, and revised citation instructions. [1] [2] [3] [4] [5] [6] [7]

Contributing Guidelines and Project Structure:

• Greatly expanded CONTRIBUTING.md:
  • Added bilingual navigation and clarified that tutorials are in docs/tutorials/en/ and docs/tutorials/zh/, with instructions to update and rebuild them after changes. [1] [2]
  • Updated project structure section to include new directories (skills/, install.sh, etc.) and explained their roles. [1] [2]
  • Provided detailed, step-by-step instructions for adding new interactive features, command-line flags, and tab-completion support, with improved shell and Python code patterns. [1] [2] [3] [4] [5] [6] [7]
  • Added explicit shell/Python style guides, testing commands, and conventions for commit messages and branch management (now rebasing on dev).

Quick Start and Example Updates:

• Improved example commands in Scripts/README.md for clarity and alignment with the latest workflow. [1] [2]

These updates provide clearer guidance for both users and contributors, ensure consistency in new feature development, and help maintain high code quality across the project.