Add new pre-commit entry

[delucchi-cmu]

Change Description

Closes #558

This PR kind of expanded...

On the PPT itself:

• Removes the sphinx-build pre-commit stage. It has been removed from the PPT config by Remove sphinx check, improve mypy check/versions. #569.
• Ran pre-commit autoupdate to update the versions of checks
• Fixes formatting and lint issues as a result of new checks

On hydrated projects:

• Adds pre-executed-nb-never-execute when you have docs and notebooks.

Checklist

• This PR is meant for the lincc-frameworks/python-project-template repo and not a downstream one instead.
• This change is linked to an open issue
• This change includes integration testing, or is small enough to be covered by existing tests

[delucchi-cmu]

You can see this in action with astronomy-commons/lsdb#1226