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Created attachment 229498 [details] the left model The two models attached are dynamic instances of the Nodes test metamodel. As the .ecore file is not aside them they can't be opened. But when comparing each other with EMF compare, it simply detects "no differences". It should detect that the models are invalid instead.
Created attachment 229499 [details] the right model
It seems like this would only require us to display an error message in the structure pane, allowing users to know that something isn't right with the "model" comparison, and that he should instead switch to "textual".
Proposal has been committed: https://git.eclipse.org/r/#/c/17201/ A message is logged, a pop-up is display with the error and the editor is closed.
Fixed in 792e66bc29b83d8e2510dfd5c54ccde91892020f