chore: Fix pre-commit on F41 and update remaining dependencies #13843
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Edit: this also updates the internal dependencies to be reasonably up-to-date enough to even successfully install. otherwise
lxml
doesn't compile on Fedora 41. Essentially without this PR, developing on Fedora is broken and thus we should merge this reasonably quickly.newer Pre-commit versions issue warnings about our config using outdated stage names. This fixes to be complaint to pre-commit v4.