You probably have to figure out how to do it with XDoclet merge files or some such.
besides removing the path what you need is META-INF/MyDescriptor.xml
I could not figure out how to do it with xdoclet either. So I generate
it and it looks like what you are getting and then I change it by hand
and add the META-INF.
I also changed my ant script to require a cmd line arg to generate
the descriptor file again i.e. -Dgen.descriptor=true