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As mentionned in the subject of this bug, EGit is creating its own custom implementation of the TypedElement interface when using the "right-click > Compare with Commit..." action (triggered when right-clicking a resource in the workspace). This means that the files will _always_ be compared as text instead of using the proper comparison engine, effectively disabling tools such as EMF Compare (that provides custom comparison engines for EMF models). Furthermore, this does not make use of the ModelProviders in order to determine whether the selected file is part of a logical model before comparing it. This second issue makes this bug a blocker for bug 354474.
Laurent, I'm sorry but I cannot reproduce this with current master. Using the History or Compare with..Commit menu results in using the EMF Compare editor to compare the resource in question. The only case I saw the text editor is if the target commit to compare with does not have corresponding file in the repository. Laurent, can you provide any steps to reproduce this? I remember some problems around a copied TypedElement but that might be fixed in the meantime.
Benjamin, I can no longer reproduce the issue with the latest master either; I guess this has been resolved by some of your other commits pertaining to the logical resources integration... Comparing with the history or from the commit viewer now properly trigger EMF Compare when the files to compare are models.
Great!