[harryswift01]

Summary

This PR moves the template's documentation to the shared CCPBioSim Sphinx theme (ccpbiosim-sphinx-theme) and the docs/source layout, so new projects start with the same setup as the rest of the CCPBioSim repositories.

Changes

• Move the documentation into docs/source, and update the Makefile and .readthedocs.yaml.
• Replace Furo and the old docs extensions with ccpbiosim-sphinx-theme and sphinx-autoapi in the docs dependencies.
• Generate the API reference with sphinx-autoapi and read the release from the installed package.
• Add a banner, quick start and section cards to the home page, with comments on what to change.
• Remove pytest-sugar, which crashes with pytest 9.2 when run in a terminal.

Testing

• Built the docs with make -C docs html SPHINXOPTS="-W --keep-going" with no warnings.
• Ran the tests and all pre-commit hooks.
• Checked the home page, the API pages and the "Edit on GitHub" links.

Impact

• New projects created from the template start with the shared theme, the docs/source layout and a generated API reference.
• Existing projects are unaffected.

Checklist

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