If you can take a look at https://github.com/jbosstools/jbosstools-hibernate/pull/5
give your comments.
I basically check when adding a file if there is a jpaFile already present for this file.
If this is the case I just return it otherwise, I delegate to the superclass. This fix
solves the duplicate listener exception (https://issues.jboss.org/browse/JBIDE-12784