Regenerate API documentation and standardise Google-style docstrings

[harryswift01]

Summary

This PR regenerates the API documentation following the recent internal restructuring of CodeEntropy and standardises all docstrings to Google-style format. It also resolves multiple Sphinx build warnings and introduces tooling to prevent future documentation regressions.

Changes

Documentation Regeneration

• Regenerated autosummary API documentation to reflect the new package structure.
• Replaced legacy docs/api.rst with generated docs/api/ module pages.
• Updated index.rst and FAQ references to align with the new layout.

Docstring Standardisation

• Migrated docstrings across core modules to Google-style format.
• Fixed reStructuredText formatting issues causing Sphinx warnings:
  • bullet list spacing
  • literal block indentation
  • definition list termination
  • unexpected indentation errors
• Updated documentation across:
  • entropy modules
  • levels modules
  • molecules
  • workflow
  • results reporting

Tooling & CI Improvements

• Updated conf.py to fully support Google-style docstrings via napoleon.
• Added rstcheck to pre-commit for docstring validation.
• Configured pre-push Sphinx build to fail on warnings.
• Updated CI docs job to enforce warnings-as-errors.
• Ensured Ruff compatibility with formatted docstring blocks.

Impact

• Documentation now builds cleanly without warnings.
• API docs are aligned with the current internal architecture.
• Future documentation formatting regressions are caught locally before push.
• CI now enforces documentation correctness as a quality gate.

[jimboid]

An important iteration on the API, keeping it updated with the codebase until we redesign the interface later. The docstrings being standardised is a great step to keeping the code in a maintainable state. The proper naming of CI is a nice addition here too which helps to keep things understandable in the process side of things. Please go ahead and merge.