Pure native scalar queries are not yet supported not seen in IntelliJ IDEA runtime

I hope that subject almost makes sense as this really doesn't I have a maven based (dropwizard) project using hibernate in intelliJ IDEA 13 that will compile and debug fine however running form a command line ala;

java -jar target/test-1.0-SNAPSHOT.jar service config/config.yml

produces the ominous;
Exception in thread "main" org.hibernate.cfg.NotYetImplementedException: Pure native scalar queries are not yet supported

yet I can run the same classes in the IntelliJ IDEA environment fine and without a problem. The only other option I seem to have is to abandon the single jar and use a monstrous classpath (which I'm not above doing) however, that seems to defeat the single jar I was hoping for. Has anyone else seen a similar type of behavior?