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For some reason, files have chevrons associated with them like they have children. This shouldn't be the case. See the attached picture.
Created attachment 176804 [details] Synchronize
Change set: http://egit.eclipse.org/r/1329 should fix this bug, but this is rather some kind of workaround then a real fix (IMHO).
Fixed with 2de643fbdda2f114ff0372699421583c0fc4d6ac. Please open another bug if you think there may be a better way to do this so we can track the issue.