If a servlet class is packaged as a compressed JAR and put in WEB-INF/lib directory of a WAR, then plan creator will fail to recognize such class.
GERONIMO-3850, you may not notice any exceptions on console, rather Plan Creator would have simply failed to detect any references/security configurations required for the web-app.
When you input such WARs to Plan Creator, you will see that after "WAR - Environment" page you will directly move to "WAR - Dependencies" page. i.e. no "WAR-References" or "WAR-Security" page will be shown even though the web-app requires certain references to be resolved or security roles to be defined.