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When manually merging a pull request the status is not updated accordingly. This is a known issue (for about 2 years already):
Until this is fixed it would be good to at least rename the button (and the corresponding message) to "close" as "cancel" is really causing a big confusion in this scenario.
Forgot to mention that the email notification should be adjusted as well.
Metadata Update from @pingou: - Issue tagged with: RFE, easyfix
Metadata Update from @pingou: - Issue assigned to pingou
Metadata Update from @pingou: - Issue set to the milestone: 5.2
Commit a350617 fixes this issue
Thanks!
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