I found one solution but I still have to wonder if there is a better way.
What I've done is hand write the hibernate mapping files so that the parent and subclasses are all in the same file. Thus I have
cat.hbm.xml --> Cat, Features, etc
dog.hbm.xml --> Dog, Features, etc
I then set up a persistenceManager which initialized different instances of itself with each of these hibernate files. Then I can call back the appropriate Configuration from the PersistenceManager by keying each configuration to the parent class.
I had to abandon XDoclet to do this but that's OK.
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