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After a repo group has been deleted once, the confirmation will not appear again, although the checkbox has not been checked. Looking at the git preferences afterwards its also unchecked there, so some code magically clears the flag.
New Gerrit change created: https://git.eclipse.org/r/152895
Cannot reproduce as stated, but the flag was also set to false when the dialog was canceled. That's fixed by https://git.eclipse.org/r/152895 .
Gerrit change https://git.eclipse.org/r/152895 was merged to [master]. Commit: http://git.eclipse.org/c/egit/egit.git/commit/?id=6665fde1e3056c69aa5a1dd9d4e17ac578890b03
Can this be closed, or is there indeed still a problem with that flag?
You are right, this can be closed. I also only had the use case of cancelling the dialog.