I have a XXX.ear file, created using Project Archive, it deploys as XXX.ear.jar/XXX.ear file on the deployment folder. It adds this XXX.ear.jar on top of the ear's structure, but the rest is just like I created.
This used to work on JBoss Tools 3.1.0.M2, I worked this around by just replacing the JBossAS plugin from the M2 version with the M4 version and worked nicely.
Steps to reproduce: 1) Create a Java Project
2) Create a EAR file using the Project Archive plugin
3) Add the archive created to the JBoss instance to be used
4) Start the JBoss, deploying the EAR
5) Open the deployment folder and see the EAR's wrong extension