Create a separate direcotry for simulation compilation.

Moved most generated files into the build directory.  All object code,
io_src realated files, and swig related files are now in build.

Realized that ICG should be creating the makefile for the io_src
code.  ICG knows which files it created.

refs #80

trick_source/codegen/Interface_Code_Gen/main.cpp

@@ -189,6 +189,10 @@ int main( int argc , char * argv[] ) {
     free(input_file_cp) ;
     free(input_file_full_path) ;
 
+    if ( ! sim_services_flag ) {
+        pa.printIOMakefile() ;
+    }
+
     // Print empty io_src files for headers that we visited, but have no class/struct information.
     pa.printEmptyFiles() ;