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Save result of EMF Compare in emfdiff file. try to open it - it's not possible, the error message is shown: "Compare failed: index=2, size=1"
Came from EMFT newsgroup - http://www.eclipse.org/forums/index.php?t=msg&goto=646145&S=03f0eb095bcfaddc04303f0524db6397#msg_646145
Created attachment 185696 [details] Exception
I couldn't reproduce this with an emfdiff of my own, I'd need a sample presenting this issue (and the models for which it has been created) in order to reproduce and (hopefully) fix this.
Closing this bug as for now, will reopen if it can be reproduced.