Fixes bug where -jar and -cp were conflicting and breaking stagegroups

When StageGroups contain stages from multiple jars, the java commandline call was being incorrectly constructed.

`java -cp <path>/* -jar <onejar>.jar` was incorrect. `-jar` will force the java command to ignore any passed classpath with the `-cp` flag. Additionally, wildcard classpaths would only work if there was no classpath at all in the manifest of any of the jars, otherwise it would crash. 

In short, I think we (me) rather failed in testing StageGroups when they were not living in the same jar.