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C git calls the pre-push hook only after the remote advertisement has been received, and rejections have been already determined. See [1]: they don't pass updates that were rejected early (or that are up to date) to the hook. JGit calls the hook in Transport.push(), before the PushProcess is even started. This is too early. [1] https://github.com/git/git/blob/e6ebfd0e8/transport.c#L1200
New Gerrit change created: https://git.eclipse.org/r/c/jgit/jgit/+/190989
Gerrit change https://git.eclipse.org/r/c/jgit/jgit/+/190989 was merged to [stable-6.1]. Commit: http://git.eclipse.org/c/jgit/jgit.git/commit/?id=90df7c123ecac9ae75a189b761a2599d5fba3565