Clean up legacy compat, dead code and duplication left by the protein/parametrization/mdp stack - #69

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, prefix-dev/setup-pixi@v0.8.8. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/