Leftover sphinx / sphinx-pythia-theme related code needs to be cleaned everywhere

[erogluorhan]

This is likely going to be a huge issue that spreads over many repositories, so I think it is good to mention it here: Despite some cookbook migration to mystmd work performed already, there hasn't been any effort made to cleanup sphinx/sphinx-pythia-theme releated code and configuration from any repositories. Leaving them where they are will definitely lead to future confusions.

[jukent]

There are a lot of great steps outlined by @kafitzgerald in ProjectPythia#462, which we'll want to create a PR to display on the website somewhere (perhaps just the myst version for now if we don't want to confuse any other contributor's yet)

Some steps that are added for cleaning up code are: removing the _config.yaml and _toc.yml from each repository.