I have two GitHub Pull Request Builder jobs on my Jenkins server. One of them is quite lightweight, it starts for every pull request and all it does is check that the code is formatted in accordance with certain requirements. It works fine, and its copies of the repository are always consistent and working.
However, my other job, which actually builds pull requests and is triggered by a magic word in the pull request comments (that is, not every pull request triggers a build), breaks its repositories very often. That is every now an again the job will fail with something like this:
+ 295dab1...86c66ff refs/pull/5681/merge -> origin/pr/5681/merge (forced update)
error: cannot lock ref 'refs/remotes/origin/pr/5686/merge': 'refs/remotes/origin/pr/5686/merge/MYPROJ-3078-my-branch' exists; cannot create 'refs/remotes/origin/pr/5686/merge'
! [new ref] refs/pull/5686/merge -> origin/pr/5686/merge (unable to update local ref)
I tried cleaning up the repo after each build (with git gc or git prune), but it didn't help. So every so often I have to go and reclone the repo.
What could be the problem? How can I fix this?