(The details about migration to 3.6 version of Hibernate are here : http://community.jboss.org/wiki/HibernateCoreMigrationGuide36 . Look at point 2)
Although not fatal to the generated Hibernate mappings (Hibernate 3.6 will read the mappings but complain about the DTD) the warning messages in the logs are quite ugly.
I have tested with my simple configuration that changing the hard-coded strings for the DTD in Java classes and Jelly template files fixes the problem.
What is done is to implement a more intelligent mechanism that would allow to generate new (Hibernate >= 3.6) and old configuration files.
A very simple patch i attached (against 1.0.6-SNAPSHOT version of the plugins)