Map<Object,Object> options = new HashMap<Object,Object>();
options.put(XMIResource.OPTION_SCHEMA_LOCATION, Boolean.TRUE);
resource.save(options)

project
 --- input
      --- metaModel.ecore
      --- instanceModel.xmi    
 --- results
      --- run1
           --- optimisedModel.xmi
      ---run2
           --- optimisedModel.xmi

public class Example {
	
	public static void main(String[] args) {
		ResourceSet rs = new ResourceSetImpl();
		Map<String, Object> map = rs.getResourceFactoryRegistry().getExtensionToFactoryMap();
		map.put("ecore", new EcoreResourceFactoryImpl());
		map.put("xmi", new XMIResourceFactoryImpl());
		
		String basePath = new File("results/run1").getAbsolutePath() + File.separatorChar;
		URI baseUri = URI.createFileURI(basePath);	
		rs.setURIConverter(new ExtensibleURIConverterImpl() {
			@Override
			public URI normalize(URI uri) {
				if (uri.isFile() && uri.isRelative() && baseUri!=null) {
					return uri.resolve(baseUri);
				} else {
					return super.normalize(uri);
				}
			}	
		});		
		
		URI ecoreUri = URI.createFileURI("../../input/metaModel.ecore");
		Resource r = rs.getResource(ecoreUri, true);
		EPackage metamodel = (EPackage)r.getContents().get(0);
		rs.getPackageRegistry().put(metamodel.getNsURI(), metamodel);		
		
		EClassifier classmodel = metamodel.getEClassifier("ClassModel");
		EObject modelroot = metamodel.getEFactoryInstance().create((EClass)classmodel);
		
		URI outputPath = URI.createFileURI("offspring.xmi");
		Resource resource = rs.createResource(outputPath);
		resource.getContents().clear();
		resource.getContents().add(modelroot);
		Map<Object,Object> options = new HashMap<Object,Object>();		
		options.put(XMIResource.OPTION_SCHEMA_LOCATION, Boolean.TRUE);
		
		try {
			resource.save(options);
		} catch (IOException e) {
			throw new RuntimeException(e);
		}
	}
}