Any JavaEE APIs should neither be in WEB-INF/lib nor in jboss-deployment structure.xml. For what's added automatically check out Implicit module dependencies for deployments - WildFly 8 - Project Documentation Editor. Anything not on that list can either be in jboss-deployment structure.xml (if it's a module) or WEB-INF/lib
Thanks for the clarification!
Also once you are doing migration, you can just paste list of jars you have in your lib and your jboss-deployment-structure.xml
and we can easier help you out what you could remove from your lib and what not