Is there a way to have middlegen to map my sets including only the Pk's and not the full objects, i.e.,

Set categoryIds;

instead of

Set categories;

?

Maybe I wasn't clear....

What I want is Middlegen to generate my mapping document so as to include a <element> or <composite-element> tag inside my sets, in such a way that my sets are loaded only with the associated primary key values, and not the entire referenced objects.

Sorry - this is not supported by Middlegen out of the box. You can change the velocity script to make it generate this by default. If you can think of a reasonable why to make it happen then I'll consider it.