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The ".uml" file contains model data, and the ".notation" file contains graphical data, both being shared by all people working on a Papyrus project. The ".di" file contains more personal data (kind of local settings), such the way windows are displayed, which diagrams are opened, and should typically not be added to a source control. Moreover, this file could be optional and automatically recreated if not present in the project.
Moving the discussion to Bug 400809 I mark this task as a duplicate *** This bug has been marked as a duplicate of bug 400809 ***