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I recently had the "User operation is waiting" dialog when pulling from a repository. In the list of waiting jobs shown in that dialog were 2 instances of "Updating file differences of commit...". Users should not see that job, e.g. it should be configured as system=true, user=false.
New Gerrit change created: https://git.eclipse.org/r/154075
Gerrit change https://git.eclipse.org/r/154075 was merged to [master]. Commit: http://git.eclipse.org/c/egit/egit.git/commit/?id=1ee69481c22915ca9c038b28f56e69ef21c106ea