WSAD contains much of the support infrastructure in the actual application server. This is why you have no copy in the EAR. For best practice migration capability between these two application servers, it would be better to place these supporting components in the JBoss instance lib directory - so if you were running the default instance, it would be server/default/lib of your JBoss distribution.
Also, the .classpath is not a file normally used by either Tomcat or Jetty so it will have no bearing. You will also find that there are some WSAD helper files that JBoss will not use. Similarly, JBoss helper files (such as jboss.xml) will be ignored in a WSAD deployment. It is a standard task for the deployment engineer to manage the deployment files when switching between application servers. Applications that faithfully adhere to the J2EE specifications will not need any re-coding.
We usually code for JBoss and develop the descriptors for JBoss. We use the WSAD deployment tool (Application Assembly Tool) to repackage for WSAD. YMMV.
Hope that helps.