chore: add manual stages to pre-commit hooks in config #670

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Run time

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Job	Run time
install (macos-latest)	10s
formula (macos-latest)	24s
test (macos-latest, 3.12)	1m 36s
install (ubuntu-latest)	25s
formula (ubuntu-latest)	17s
test (macos-latest, 3.11)	1m 18s
test (macos-latest, 3.10)	1m 40s
test (macos-latest, 3.9)	1m 4s
test (ubuntu-latest, 3.12)	1m 25s
test (ubuntu-latest, 3.11)	1m 20s
test (ubuntu-latest, 3.10)	1m 22s
test (ubuntu-latest, 3.9)	1m 25s
	12m 26s