Update pre-commit

[jonburdo]

Our .pre-commit-config.yaml has not been updated in a long time. It also isn't in sync with what we use in Makefiles and CI.

For instance, the ruff version used in the pre-commit is very old and has some quirks.

We may want to simply remove it, but let's check if there's any tools from it that we want to move to Makefiles.