When a Java package is moved from one Eclipse source path to another using Package Explorer, Eclipse does not actually move the folder. Eclipse instead deletes and creates the package's folder structure. Thus, the Synchronizer View reflects this as an Outgoing Deletion rather than a changed status.
If you perform the move in the Navigator View, the folder history will be maintained; however, this is not Java Refactoring and Eclipse will not update the references to moved classes.
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