The problem with everything is that the inheritance hierarchy is not mapped, instead it is read at runtime from the classes themselves. So, when you're generating the initial entities from the mapping information, you don't have that information, so we can't properly generate a class with the "class ClassName extends SomeOtherClass" because we simply don't know it.
To work around it all you have to do is manually create the file with the empty class inside of it, extending the class you want. When you run the orm:generate-entities again, it can properly read the subclasses of every entity and the generation will update the classes existing classes properties and methods instead of trying to generate a new class.
Does that clear things up? I think the only way to fix it would be to allow the user to manually specify the all the inheritance information in the mapping information instead of reading it at run-time. That way we have all the information about some entities even before the actual classes exist and we can generate the right code then.