1) Install JBoss Tools version 4.0 (Juno)
2) Create a new workspace
3) Select Java EE Eclipse perspective
3) Define a new JBoss Server and new JBoss Runtime with 6.x server adapter from JBoss Tools (using jboss-6.1.0.final)
4) Create an EJB Project (Targeted runtime: JBoss 6.x, EJB module version: 3.1, default options)
5) Click with right mouse button on the server, than select "Add and Remove...".
6) The EJB project on the left list. It is still possible to deploy the EJB project into the server (See image 0)
7) Create a Dynamic Web Project (default options)
8) Put the EJB project in the Deployement Assembly of the Dynamic Web Project (see image 1)
9) Click again with right mouse button on the server, than select "Add and Remove...".
10) The EJB project is no more present in the left list. It isn't possible to deploy the EJB project into the server (See image 2)