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Currently, the EMF Compare copier only takes DiffModels into account. This is a legacy from the time EMF Compare did not consider whole resource sets for the comparison; and causes random bugs due to the order in which differences are merged. For example, if a given comparison involves three resources, we have one DiffResourceSet containing three DiffModels. Merging a difference from the first of these DiffModels creates a Copier for it. If I then merge a difference from the second DiffModel, the Copier is reset (!) and a new one is instantiated for the second DiffModel. This implies that all information from previously merged differences are lost. This also implies that the Copier won't be able to find diff information if they are located in other DiffModels; preventing most of its logic to be set in motion.
This has now been fixed on master.