pre-commit: Update pre-commit config and tools versions

[echoix]

Multiple pre-commit tools were not up-to-date.

Most annoyingly, Flake8 didn't run at all with a Python 3.12 (by default) workspace, and had a version of a couple years ago.

Since we will be changing the black yearly version soon, I made a round of changes that should be integrated before this.

I added some additional tools from the https://github.com/pre-commit/pre-commit-hooks, and enabled black formatting for jupyter notebooks.

Someone with admin rights should enable the pre-commit checks from this issue https://github.com/OSGeo/grass/issues/3255 in the short-term, as there were already some files that were out of date. (Excluding jupyter notebooks). Should I do a separate PR for these 13 files? If setting up pre-commit.ci is too complicated (meaning only one person can really administer the changes), I suggest their other way of running pre-commit, by GitHub Actions workflows so we could at least be able to do PR for improving the configuration.