Add initial MkDocs documentation site

[eliantiudic]

Summary

This PR adds an initial MkDocs documentation site for AToM-OpenMM using Material for MkDocs.

It includes:

• mkdocs.yml with site navigation, theme settings, logo/favicon, search, code copy, and MathJax support
• New documentation pages for installation, tutorials, user guide, theory, API reference, troubleshooting, and contributing
• User-guide pages for current ABFE/RBFE workflows and YAML configuration files
• A command-line API reference for the main AToM-OpenMM tools
• A docs conda environment in docs/environment.yml
• A GitHub Actions workflow to build docs on PRs and deploy from master
• site/ added to .gitignore

How to Contribute to the Docs

Create the docs environment:

conda env create -f docs/environment.yml

Activate it:

conda activate atom-openmm-docs

Preview the site locally:

mkdocs serve

Build and check the docs before pushing:

mkdocs build --strict

Most content lives under docs/. Navigation is controlled in mkdocs.yml.

Deployment

The docs workflow runs mkdocs build --strict on pull requests.

After this PR is merged into master, GitHub Actions will build the site and deploy the generated site/ artifact to GitHub Pages.

For deployment to work, GitHub Pages must be enabled in the upstream repository settings:

Settings → Pages → Build and deployment → Source: GitHub Actions