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GMFGen files for Papyrus diagrams use relative path to reference genmodels: "../../../plugin/org.eclipse.uml2.uml/model/UML.genmodel" "../../../plugin/org.eclipse.gmf.runtime.notation/model/notation.genmodel". Note that both of models are located in plugins. Because of it if the user's attempts to open a GMFGen model in SVN fail - EMF looks for the models using the relative paths, in CVN, and cannot find it. As a consequence, it's not possible to compare Papyrus gmfgen models using EMF Compare. Use "platform:/plugin" uri instead, e.g. "platform:/plugin/org.eclipse.uml2.uml/model/UML.genmodel".
Fixed for Class diagram
The "../../.." URIs will come back after each save action. The replacement of relative URIs with platform:/ based URIs is the responsibility of the Editor, which is provided by GMF Tooling (i.e. specific Save Options to add in the resource)