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ResourceSet.createResource(URI) returns "null" in standalone if there is no resource factory registered for that URI's file extension. In the last version of EMF Compare, we automatically registered a new XMIResourceFactoryImpl() when there wasn't any, thus we never returned null; yet with my latest refactoring this default factory is no longer registered, provoking NPE with some implementations in standalone mode.
The fix has been commited and will be available in 3.0.1RC2.
Should have read "1.1.1RC2"