Maintenance cleanup

[blink1073]

• Use Flake8-pyproject to avoid needing a .flake8 file
• Use mdformat instead of prettier
• Add pyproject validation
• Rename readthedocs config file to recommended name
• Add manual pre-commit check in CI
• Add rollup check that can be used for branch protection and auto-merge
• Other minor workflow cleanup

[blink1073]

@kevin-bates the backticks were added by mdformat, if you'd like to push changes that would be appreciated. You can run pre-commit run mdformat locally as you are iterating.