Oops. Arguments didn't load into applications with non-plugins (basically everything except the GATK).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@617 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java

@@ -151,6 +151,7 @@ public abstract class CommandLineProgram {
             else {
                 parser.parse(args);
                 parser.validate();
+                parser.loadArgumentsIntoObject( clp );
             }
 
             // if we're in debug mode, set the mode up