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This has happened because first PR was merged successfully, and it changed the master branch. Then (during the next PR merge) the destination branch has not been updated automatically. Such updates failed and I used to rerun the same code once more.
githubfile provider does not have a way to rebase each PR before the merge.
In the meanwhile, I will run script to remove such branches from all repositories.
It would be nice to remove githubfile's branches after PRs are merged.
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