// set up the load option:
set.getLoadOptions().put(XMLResource.OPTION_RECORD_UNKNOWN_FEATURE,
    Boolean.TRUE);

// sample upgrade function:
private void processModelUpgrades(Resource resource) {
    if (!(resource instanceof XMLResource)) {
        return;
    }
    Map<EObject, AnyType> extensions = ((XMLResource) resource)
            .getEObjectToExtensionMap();
    MApplication application = (MApplication) resource.getContents().get(0);
    TreeIterator<EObject> it = EcoreUtil.getAllContents(resource
            .getContents());
    while (it.hasNext()) {
        EObject obj = it.next();
        if (obj instanceof MBindingTable) {
            AnyType anyType = extensions.get(obj);
            for (Entry feature : anyType.getAnyAttribute()) {
                if (feature.getEStructuralFeature().getName()
                        .equals("bindingContextId")) {
                    MBindingContext root = getBindingContext(application,
                            (String) feature.getValue());
                    ((MBindingTable) obj).setBindingContext(root);
                    System.out.println("set " + root);
                }
            }
        }
    }
}