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Scenario to reproduce with EcoreTools : 1. Create a Modeling Project named MP1 2. Add a semantic resource MP1.ecore and select Design viewpoint 3. Create a Class Diagram 4. Create a Modeling Project named MP2 5. Add a semantic resource MP2.ecore containing MP2EClass and select Design viewpoint 6. From MP1 Add MP2.ecore as semantic resource through "Add Model" contextual action on "Project Dependencies" 7. Drag'n drop MP2EClass from "Project Dependencies" tree to diagram to have a view displayed for MP2EClass 8. Now try to remove the MP2.ecore dependencies through "Remove Model" contextual action => KO the action is enabled but should not as its content is yet referenced by other content. 9. Save, close and reopens the MP1 Modeling Project => the session is dirty and the MP2.ecore dependencies is yet here. This is a regression it was working before Sirius.
Triaged and marked as regression.