I don't use MyEclipse, so I can't help you with that. But here are some suggestions:
a) Never use MyEclipse (or an other IDE) to build and deploy your app; instead use Ant or Maven. Then you will have more control over what is built (rather than having the IDE be too "helpful" and mess things up.)
b) If I were doing this in Eclipse, I would install the JBoss Tools plugins. One of the Tools helps with Hibernate development. And since the Tools understand Jboss AS, they properly package apps thatuse Hibernate and thus avoid the situation you find yourself in. I don't know if Jboss Tools work in MyEclipse, but it would be worth a try.
Both of the above suggestions prevent the Hibernate JARs from being packaged with the app, thus avoiding having to use a classloader repository.
Unfortunately, the choice of MyEclipse to IDE was not mine and is out of my control.
MyEclipse has hibernate and Jboss integration , but don't prevent de jars from being deployed. I don't know why and don't make sense but...
I solve the problem temporarily and i was able to deploy the project but i will take your advice and start to use Ant or Maven to deploy.
For WAR Project use jboss-web.xml and put it into WEB-INF Folder. It will be not considered by JBoss if it is in META-INF.
For EAR Project use jboss-app.xml and put it into META-INF Folder.