Fix pre commit hook

[Lee-W]

In the previous pre-commit PR, I add the wrong stages argument into the .pre-commit-hooks.yaml. It should be defined on the user side. I'll also update the document.

BTW, I notice it didn't bump the version and release on the previous PR.

[Kurt-von-Laven]

@Lee-W, I believe it was correct before. Hooks can confine themselves to particular stages when they know they would only be useful in those stages. Maybe one could argue that there is value in adding prepare-commit-msg to the list of stages in which one could run the hook, but unless someone comes forward with a good reason to do that, I would wager even that case is more likely to be a misconfiguration. Confining the hook precludes what I suspect to be a far more likely misconfiguration, where the user accidentally runs the hook pre-commit, for example. I have opened #514 proposing to revert this revert, so please let me know if I am missing something.