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I'm having the same problems and saw similar problems with Atlassian's Stash and Fisheye when they moved to jgit. There was some horrible / stupid hacks that I had to do to get it to work. I would vote not using jgit as this was working properly before. For as long as I have used Jenkins + Git (+5 years), I have never experienced a problem with the old implementation. If you are seeing memory / output problems, it's probably not from Git.