I was having issues with Hibernate, specifically the meta model stuff.

That's because my persistent classes were scattered across 3 packages:

support: base classes everything inherits from
gen: generated source code my modeling tool spits out.
main: my customized code.

So every entity was in 3 packages:

support: mappedsuperclass
gen: mappedsuperclass extends support
main: entity extends gen

The problem I was having with the metamodel was that it wasn't generating any extends lines for the superclasses.

My problems all went away when I listed everything in orm.xml. The annotations still set everything, but now Hibernate can find everything.