Looking at the naming dependencies, they are in the core project, and include:
org.jboss.naming.ENCFactory - java:comp management
org.jboss.naming.JavaCompInitializer
org.jboss.naming.NamingContextFactory - uses lastInitialContextEnv ThreadLocal
org.jnp.interfaces.NamingContext
org.jnp.interfaces.MarshalledValuePair
org.jnp.server.SingletonNamingServer - testing
org.jboss.naming.Util - should be using org.jboss.util.naming.Util from jboss-common-core. I have replace this.
The naming server has already been pulled into https://svn.jboss.org/repos/jbossas/projects/naming/trunk/jnpserver by Anil, so we should just be able to switch to that, and so can jbossas.
I released org.jboss:jnpserver 5.0.0.Beta4 and have replaced the org.jboss.jbossas:jboss-as-naming with it in the ejb3 poms and eclipse files.