Try following code on test/Test.java:

... get source cookie ...
SourceElement se = cookie.getSource();
ClassElement ce = new ClassElement();
ce.setName(Identifier.create("test.Test", "Test"));
se.addClass(ce);
ce = se.getClass(Identifier.create("test.Test"));
System.err.println("ce = " + ce);
ClassElement[] ces = se.getClasses();
for(int i = 0; i < ces.length; i++) {
  System.err.println("ce[" + i + "] " + ces[i].getName() + ", full = " +
    ces[i].getName().getFullName());
}

I would expect following output:

ce = <textual representation of class>
ce[0] Test, full = test.Test

But I've got:

ce = null
ce[0] Test, full = Test
ce[1] Test, full = test.Test.Test