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repo.index.commit() is a custom implementation which doesn't run hooks indeed.
It should either do that, or clearly state that it doesn't, providing a git-command workaround instead.
Please note that even though commit hooks are implemented now, they are only tested and verified to work on posix.
If you need it on windows, please let me know what kind of hook you are running there, just because I am unsure how any script is run on windows by git at all.
repo.index.commit("commit") not run hooks
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