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Basically, rebasing will put you into a state where you have a local commit with a different sha1 from your remote commit of the same patch. So don't do that. Instead, use git merge upstream/master if you need to pull in new commits from rapid7's fork. But! As @tpope explains, it may not be worth the clogged up history, so don't do that either. http://tbaggery.com/2008/04/18/example-git-workflows-maintaining-a-long-lived-topic-branch.html