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After the discovery of Java and Inventory models, we get the main model (JavaApplication), however the resource set doesn't "contains" the resource of Java model (*.javaxmi). If you use a query that use the resource set to link a java element with a source element (like class GetASTNodeSourceRegion), you get a different behaviour from one inside MoDisco browser.
To reproduce this bug, try the test associated with bug 332323 without reloading and resolving the model of JavaApplication.
Hello, I'm really sorry, but the year we have to focus on the move to EMF Facet. We may not be able to work on this bug. That's why cannot plan this bug for the Juno release. Regards, Gregoire Dupe