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In the Transport(Repository local, URIish uri) constructor. As a result the hook's stdout will always go to System.out. Might be (part of) the cause of bug 536659.
The variable hookOutRedirect is actually never assigned to anything ... But I don't think this is part of the cause for bug 536659 because this is only relevant for pre push hooks and bug 536659 is about pre commit hooks.
This might also be something for JGit 6.0.
New Gerrit change created: https://git.eclipse.org/r/c/jgit/jgit/+/196452
Gerrit change https://git.eclipse.org/r/c/jgit/jgit/+/196452 was merged to [master]. Commit: http://git.eclipse.org/c/jgit/jgit.git/commit/?id=71af0d6a5c4417a9c9c6523d4aa811579d8c867f