I would propose additions to the hibernate-configuration-3.0.dtd, to make the following possible.
Code:
<mapping path="/dev/p2pgames/modules">
<include name="p2p.games.*" />
<exclude name="p2p.io.*" />
</mapping>
Where "include" elements would declare classes with wildcards to include, and "exclude" elements ignore those classes in the path. If the body of "mapping" is empty, all classes would be included.
This could also be applied to the "jar" and maybe "package" attributes, but I don't know enough about them. I also don't know the future of the ejbconfiguration, as you stated.
So let me know if you want me to proceed. If this is not dirty enough, I have another, dirtier idea.