Using AMP with sub-packages is an essential thing. So I checked out AMP from svn repository and made a quick (and dirty ?) improvement to be aware of subpackages.
I didn't test it very much, just made the modification in AppFuseGeneratorMojo and tryied it in a "core" and "web" project and it worked.
It was a really small modification, I think it can be integrated easily (well the hard part is testing, isn't it ?).
The modified class is in attachment.