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If you compare 2 GIT revisions of a Papyrus diagram (di), EMF Compare throws an IndexOutOfBoundsException because it does not succeed to find the referenced Diagram object (of the notation resource) from the Di resource in the revision to compare with. If you add notation files as content type in plugin.xml, you will be able to compare 2 notation files but you will get the same resolving problem between the objects of the notation resource and the ones of the semantic (UML) resource. I attached a data set in a local GIT repository to reproduce the issue. - On model.di, compare with commit "init".
Created attachment 210735 [details] Data set
The resolution of inter-model dependencies is done through the ModelProvider API; here the failures comes from us not being called, and thus not being able to resolve the location of the remote model. This cannot be fixed as yet since Git is not using the necessary APIs from Team.
*** Bug 361781 has been marked as a duplicate of this bug. ***
This is fixed in EGit now.