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If the git repository in a merging state with conflicts, the differences reported by the merge viewer are incorrect. The repository from this attachement can be used to reproduce the issue: https://bugs.eclipse.org/bugs/attachment.cgi?id=245474 Steps: - import repository and the project in the workspace - select the model.uml and "Compare with > Branch..", then choose the branch "conflicting-change" - open the comparison from the "Team Synchronizing" perspective On each of the two branches(master and conflicting-change), the same element(a UML Class) has been renamed. However, the reported differences look as if the contents of the renamed element have just been added to the model. If the repository is reset (such that the state of the repo is no longer "merging with conflicts"), the differences are reported correctly: a rename on each branch.
The problems seems to come from Egit. I opened Bug 464667 and will continue to investigate.