This is a common issue. From the MDT/UML2 FAQ :
resourceSet.getPackageRegistry().put(UMLPackage.eNS_URI, UMLPackage.eINSTANCE);
resourceSet.getResourceFactoryRegistry().getExtensionToFactoryMap().put(UMLResource.FILE_EXTENSION, UMLResource.Factory.INSTANCE);
Map uriMap = resourceSet.getURIConverter().getURIMap();
URI uri = URI.createURI("jar:file:/C:/eclipse/plugins/org.eclipse.uml2.uml.resources_<version>.jar!/"); // for example
uriMap.put(URI.createURI(UMLResource.LIBRARIES_PATHMAP), uri.appendSegment("libraries").appendSegment(""));
uriMap.put(URI.createURI(UMLResource.METAMODELS_PATHMAP), uri.appendSegment("metamodels").appendSegment(""));
uriMap.put(URI.createURI(UMLResource.PROFILES_PATHMAP), uri.appendSegment("profiles").appendSegment(""));