which version of jboss tools ?
undeploying from server view should remove everything - unless the server is locking some jars.
stop the server and look in the deploy folder for anything left over from the deployment.
The jars have miraculously vanished now! :)
but they were quite around in the java.j2ee section, inspite of me removing the jar from the server view!
well maybe the server just hadn't discovered that the files were gone - there is a few seconds delay and then the undeploy need to happen.