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The ModelCompareEditorInput resolves proxies in different ResourceSet. The issue is when left/right/ancestor models are linked to the same model (e.g. profile) it results in IOOB. The issue seems to be in the org.eclipse.emf.compare.ui.editor.ModelCompareEditorInput.DispatchingCrossReferencer.crossReference(EObject, EReference, EObject) method. You should use three "if" instead of "else if". Regards,
This was failing in the particular case of opening emfdiff files that represented the comparison of models referencing a common third-party model (for example, profiles). This is now fixed on master.