confine pre-commit to stages (#3940)

See https://pre-commit.com/#confining-hooks-to-run-at-certain-stages



> If you are authoring a tool, it is usually a good idea to provide an appropriate `stages` property. For example a reasonable setting for a linter or code formatter would be `stages: [pre-commit, pre-merge-commit, pre-push, manual]`.

Co-authored-by: Jelle Zijlstra <jelle.zijlstra@gmail.com>