Implements Read the Docs infrastructure to generate API documentation
directly from code docstrings. Replaces static modules.md (1200+ lines).
New structure:
- docs/_source/conf.py — Sphinx configuration (furo theme)
- docs/_source/index.rst — Main TOC
- docs/_source/api/*.rst — Module groups (substrate, storage, retrieval,
qa, distill, mesh, cli)
- docs/_source/Makefile — Local build targets
- docs/_source/README.md — Documentation on building and extending
Makefile integration:
- make docs-api — generate HTML (output: docs/_source/_build/html/)
- make docs-api-clean — remove build artifacts
Build output (40 HTML files):
- API module reference with docstrings
- Source code links (:viewcode: extension)
- Full-text search index
- Module index (genindex, py-modindex)
Sphinx installed in venv as dev dependency. HTML is browseable at
docs/_source/_build/html/index.html (open in browser after build).
This justifies the deletion of modules.md: code docstrings + Sphinx
autodoc = automatically-generated, always-current API reference.