Create a separate directory for simulation compiliation.

Made some adjustments for sims larger than the ball sim.
Make some changes to handle library packages such as JEOD.  Also
removed some dead code.

trick_source/codegen/Interface_Code_Gen/main.cpp

@@ -193,9 +193,6 @@ int main( int argc , char * argv[] ) {
         pa.printIOMakefile() ;
     }
 
-    // Print empty io_src files for headers that we visited, but have no class/struct information.
-    pa.printEmptyFiles() ;
-
     // Close the map files
     pa.closeMapFiles() ;