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If a folder is renamed in the file system and then a refresh local is performed in Eclipse, the outgoing deletions do not appear. This is because the move/delete hook cannot do its magic. i.e. it cannot prevent the folder deletions and let only the file deletions through.
Are you getting the deletion notification via move/rename/delete though?
We get notification in the deltas but not in the MoveDeleteHook. The problem is that it is the MoveDeleteHook that sets the deleted folders up to be outgoing deletions. Since a deletion in the file system cannot be handled this way, it is probably best to say that if a user deletes a folder from the file system, they will see the change as an incomming addition in the sync view (as we had before). The only action I would take here is to create a test case that ensures that this scenarion works as we expect.
Fixed
Works as described.
