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There is a problem with UnitApplication's undo() method: When a UnitApplication is un-done (either manually or automatically when it fails), certain references can change their order. This changes the graph and can lead to Rules or TransformationUnits acting unexpectedly, even though loading the model graph, executing a UnitApplication and calling undo() should be equivalent to just loading the model graph.
The correct order of eobjects in reference lists should now be correctly restored for undo() and redo().
I have reverted the changes for now and reopened this bug. The update broke more than it fixed.
The new bugs should be fixed and undo() should work. I leave this bug open for now, in case some more problems occur.
It seems to work fine now.