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If an error occurs on stdout, e.g. device full, JGit will not notice and happily exit with 0. This is because it uses a PrintWriter and does not check it's status. JGit should exit with a non-zero exit code, possibly as soon as the error occurs.
Fixing this would probably require an API change, e.g. not using PrintWriter for out.
Fix a while ago in caa362f20df1169e4a677648dce2af29d63cbcec