So what I do is to separate lib and deploy:
conf/jboss-service.xml:
<service>
<classpath codebase="${jboss.common.lib.url}" archives="*"/>
<classpath codebase="applib" archives="*"/>c
<classpath codebase="${jboss.common.lib.url}" archives="*"/>
<classpath codebase="applib" archives="*"/>
conf/bootstrap/profile.xml (also farm will be found here but we do not use it):
<property name="applicationURIs">
<list elementClass="java.net.URI">
<value>${jboss.server.home.url}deploy</value>
<value>${jboss.server.home.url}appdeploy</value>
</list>
</property>
To separate the conf directory I suppose to find something like '${jboss.server/home.url}/home' or ${jboss.server.config.url} but I don't find something.
Also a look into the sources does not offer a configuration parameter for this.
So I'm also interested to find it out.