Run the following code for a FileObject owned by the attached project:

------%<-----
// FileObject fo

final ClasspathInfo cpi = ClasspathInfo.create(fo);
final ClassIndex index = cpi.getClassIndex();

JavaSource.create(cpi).runWhenScanFinished(new
CancellableTask<CompilationController>() {
    public void cancel() {
    }
    public void run(CompilationController controller) throws Exception {
        System.out.println("Finding usages");
        ElementHandle<TypeElement> entityHandle =
ElementHandle.create(controller.getElements().getTypeElement("javax.persistence.Entity"));
        for (ElementHandle<TypeElement> found : index.getElements(entityHandle,
EnumSet.of(SearchKind.TYPE_REFERENCES), EnumSet.of(SearchScope.SOURCE,
SearchScope.DEPENDENCIES))) {
            System.out.println("Found " + found);
        }
    }
}, true);
------%<-----

No "Found" lines will be printed. It starts working if you move the
"getClassIndex()" line inside the task.