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GitHub staff here. Thank you for the bug report. This was caused by a new feature we are rolling out. We have deactivated it for the moment, and a permanent fix for this issue is in the merge queue. It is safe to rebase again.

If you have existing pull requests with redundant commits, it should suffice to close and then re-open the pull request. This causes the system to recompute the PR base commit and it should then display correctly.

Sorry for the trouble, and thanks for letting us know.

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@keith
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@pierresisson
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@nhtyy
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Answer selected by alalazo
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@nhtyy
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@nhtyy
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