[EPIC] Restore clean CI gates in staged order

[Cubits11]

Purpose

Restore CI health in staged order without mixing unrelated failures.

Current Gates

1. Docs strict build
2. Pytest collection
3. Ruff
4. Mypy staged strictness

Known Problems

• Missing mkdocs.yml
• Broken strict docs links to generated figures
• Missing runtime/test dependencies such as pandas, scipy, and matplotlib
• Full mypy currently applied too broadly across research and legacy modules

Correct Order

1. Fix docs build
2. Fix dependency extras so tests collect
3. Separate strict-kernel mypy from relaxed research/legacy checks
4. Only then begin deeper source refactors

Definition of Done

• Docs build passes with python -m mkdocs build --strict
• site/ is ignored
• Test collection no longer fails from missing packages
• CI install target is documented
• Mypy is staged by package/layer

Child Issues

• Add MkDocs config and fix strict docs links
• Define test and type extras in pyproject.toml
• Update CI install command
• Add staged mypy configuration
• Document local dev setup

Notes

This epic should not include math refactors. Its goal is to make the repo’s gates honest and staged.