JBIDE-18094

We check the run mode (ie, run vs debug vs profile) when doing our publishes now... ie publishes when debug mode will not auto-restart modules.  Because of this I had to identify all areas where we WEREN'T keeping it accurate. Before that, we set it in some places, but, since we never checked it or used it, it was kind of a no-op. We set a variable we never used or checked. 

Now we check it, so now we need to make sure it's accurate.