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TL;DR: Conflicting additions that don't actually exist get stuck in view. Behavior: After I Pull, if the pull contained moves (i.e. refactoring a package), the Pull works fine on disk but the Synchronize view retains a conflicting addition (red arrow with plus sign) for each file that has been moved. There is no way to get rid of them other than to delete the synchronization and make a new one. A 'git status' on the command line show up-to-date with no changes. Workaround: Unpin and delete the Synchronization and make a new one.
Found an additional workaround: In the Git Staging view, move the entries from staged back to unstaged a few times and they disappear.