When an archived ear which includes an exploded war is deployed in EAP 6, the application seems to be deployed successfully but it returns status code 404.
1. Start EAP 6 standalone mode
2. Put the attached test.ear to $JBOSS_HOME/standalone/deployments
3. Access the web application
curl -v http://localhost:8080/test/index.jsp

JBoss returns status code 404.
JBoss returns actual response of web application's content.

Additional info:

Same application works in EAP 5. When an application is an exploded ear which includes an exploded war, it works in EAP 6.