sorry I'm a bit confused here, what is the issue?
The problem is . . . there are a number of ways to deploy a webapp under Tomcat. There are also ways of doing it under JBoss. What are the rules for resolving possible conflicts? If I have a webapp named, I don't know 'Muffins', and I have a copy of Muffins.war in $CATALINGA_HOME/webapps, and another copy in $JBOSS_HOME/server/default/deploy, then which one wins?
This is just an example. In general, JBoss is designed to contain a webapp container. JBoss also itself handles some webapp container duties (with deployment being one). I've never seen attention paid to resolving these conflicts. I'm not saying that no attention has been paid, but if it has I would like to see it.
well, with jboss there is one way to deploy and that is through jboss' deploy directory.
Generally anything you do in the catalina sub-directories will be ignored.
If you have an embedded web-container best to just ignore it is there and let jboss take care of the rest.