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If I modify a file and save it, the Synchronize view captures that my local copy of the file has been modified. If I modify the file back to its original content and save again, the Synchronize view still indicates that this is an outgoing file. If I open in the compare editor, the Java Structure Compare indicates No Structural Differences. From the Synchronize view, the Update menu item is greyed out but the Override and Update menu item is not but from the Package Explorer view, I can run Team -> Update. My expectation is that the Synchronize view should be smart enough to recognize the file is the latest and greatest without my having to update.
The proper command to use in this case is Clean Timestamps. There is a request to have this happen at specific times. As you say, one of those times may be when opening an editor from Sync view (although there is an overhead associated with this so it is probably better to associate it with background tasks such as bulding). *** This bug has been marked as a duplicate of 75574 ***