It looks like there are multiple hibernate.jar in your classpath. I sugguest you to make sure there is unique version of hibernate are using.
in my opinion, hibernate that is shiped with jBPM 4.3 should be good enough and you should not mix libs from jBPM 3 with 4.3.
If it comes to j2ee library, could you provide some more information about how you are going to execute your process?
By console, do you mean that you are executing from command line or BPM console?
If you will execute your process from a container (JBoss AS) j2ee lib will be available on runtime.
Regarding hibernate, I'm trying to determine whether applications that depended on hibernate3 would break using the new jars. Is there a way to verify this without just trying to run them?
I meant that I am executing my program command line. I don't plan on executing from a container.
As far as I know hibernate included in jbpm 4.3 is 3.x.x so it should be quite ok to use it instead of the one bundled in jBpm 3.x but the easiest would be to check hibernate docs about these two versions.
About j2ee.jar perhaps you don't need to include complete package of j2ee but only required parts of it (jta, ejb, etc) that can be found as separate jars as well.