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Sapphire diagram editor uses Sapphire model and it saves node/connection layout info in a .layout file. When the diagram editor is open, it actually reconstructs the diagram using the Sapphire model and the layout file. EMF based diagram model used by Graphiti is not really needed. We should attempt to remove the .xml file corresponding to the Graphiti diagram model. It's not only inefficient but also creates maintainence issues with the additional file. For example, when a diagram is being edited, if the .xml file is accidentally deleted, then the diagram editor would enter into an unusable state.
Fixed by using a "virtual" uri for the Graphiti diagram model
Developer should no longer see the .xmi file in the .settings folder
verified with 0.3.1.201109261654
Closing based on Raj's verification.