Apply `ruff` default rules to repo, update `uv` (#4926)

* Start making ruff / lint fixes

* More lint changes

* More updates

* Fix lock file and update uv

* Delete unneeded changelog

* Fix CI

* Merge

* Fix lock file

* Update line length to 120

* regenerate bootstrap_gen

* Revert "regenerate bootstrap_gen"

This reverts commit f010f9a9b598adbdd709d254baec16db427c6b45.

* Revert "Update line length to 120"

This reverts commit b24a8cf6e53f1250a8671ae83550f98047cf39c1.

* Fix lint issue

* Add rules back in to extend select