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Lots of NPE occurs while using Papyrus. Most of them are easy to fix and should be dealt with very quickly. You may reuse this bug if you encounter one, telling in this bug and in the commit comment more details about the fixed NPE.
Fix NPE while opening class diagram with associations loaded, but linked to a not loaded element. The equals comparison must be performed with EcoreUtil.equals Concerned methods are org.eclipse.papyrus.diagram.clazz.custom.helper.AssociationEndSourceLabelHelper.getUMLElement(GraphicalEditPart) and org.eclipse.papyrus.diagram.clazz.custom.helper.AssociationEndTargetLabelHelper.getUMLElement(GraphicalEditPart) commit 5412 on trunk, 5411 on 0.8.X
I close this task which is too generic (And there aren't so many NPEs anymore)