I am also having the similar kind of issue.
As an ugly temporary hack to get it to compile I just copied the jars to the old locations so that the IDE would work.
I'm having what I think is the same problem.
I created a new EJB Project with jboss-4.0.4.CR2 and there is a jar missing from the JBoss EJB3 Library: jboss-4.0.4.CR2/server/ejb3/deploy/ejb3.deployer/hibernate3.jar.
There doesn't seem to be any way to fix the Library set because when I try to configure it it just asks me which JBoss configuration I need to use.
Have I screwed up or are the JBoss Eclipse people not in sync with the EJB3 people?
I had a similar problem the first time I installed jboss-4.0.4.CR2. The thing that fixed the issue for me was installing the jboss-4.0.4.CR2 through the installer jar and selecting EJB config while installing. The installation prompts you for what kind of installation config you want.
Further when you are setting up the new jboss config don't forget to select the new jboss-4.0.4.CR2 directory as your jboss home.
If you notice after jboss-4.0.4.CR2 is installed the default server configuration has the required jars at the required places.
I hope this helps.
I tried with the mentioned patch and also with the nightly build but in vain.
Please give me a solution.
The fix works fine.
As I had this problem again with the latest JBoss-IDE release and the final JBoss 4.0.4, here's the solution for everyone stumbling here through the search:
You have to install Jboss via the installer, and select the EJB3 package. If you select the "All" configuration, EJB3 is NOT installed, dispite the name.