[harryswift01]

Summary

This PR moves the prepmd documentation to the shared CCPBioSim Sphinx theme (ccpbiosim-sphinx-theme) and generates the API reference with sphinx-autoapi.

Changes

• Replace Furo and the old docs extensions with ccpbiosim-sphinx-theme and sphinx-autoapi in the docs dependencies.
• Set the theme in conf.py, read the release from the installed package, and remove the autodoc mocks and repeated settings.
• Generate the API reference with sphinx-autoapi instead of the committed sphinx-apidoc files.
• Add a banner, quick start and section cards to the home page, with short labels in the navigation.
• Fix the score_pdb_map docstring so its arguments render.
• Ignore docs/build, the folder the Makefile builds into.

Testing

• Built the docs with make -C docs html SPHINXOPTS="-W --keep-going" with no warnings.
• Checked the home page in light and dark mode, the guide and API pages, and the "Edit on GitHub" links.

Impact

• Docs changes, plus a docstring fix in prepmd/point_cloud.py.
• The API reference now has one page per module and is generated on each build.
• API page URLs change from api/... to reference/....

Checklist

• Tests added or updated
• Documentation updated
• If dependencies in pyproject.toml changed, the lower bounds were reviewed deliberately

[jimboid]

Looks great!