When creating J2EE projects using JBoss-IDE the WEB-INF and META-INF folders are not created until after the first time you execute XDoclet, and then they are only created if you have actually performed the configuration required for their creation.

http://wiki.jboss.org/wiki/Wiki.jsp?page=JBossIDE

If you work through the tutorial available from the link above you will see how to create an EJB, a simple web application all bundled together for deployment as an EAR archive. The tutorial also shows how to debug your deployment.