Fix fragment parsing and placement bugs; neighbor lists, load balancing, ligand options - #28

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, conda-incubator/setup-miniconda@v3. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/