To undeploy an application using File System deployment, the application's associated .deployed marker needs to be removed. Once the .deployed marker is deleted, the application is stopped but then immediately readded/restarted without triggering it with a .dodeploy marker.

I've attached a .war to reproduce.
Copy servlet_js_servlet_web.war $JBOSS_HOME/standalone/deployments
touch servlet_js_servlet_web.war.dodeploy
rm servlet_js_servlet_web.war.deployed

The .war can never be undeployed.