Fix core correctness, storage atomicity, and MCP setup - #4

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@v4, actions/setup-python@v5, actions/upload-artifact@v4. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/