Standardize directory names

Found that on the Mac ICG was ignoring all of header files comments in ${TRICK_HOME}/include because it had the relative directory "include" listed as a system path.  Comments were only processed if it wasn't in a system directory.  Changed the check to use our function that checks to see if a header is in user or Trick code, basically the same check, but it only uses full paths and doesn't get confused with "include".

refs #63

trick_source/codegen/Interface_Code_Gen/main.cpp

@@ -142,7 +142,7 @@ int main( int argc , char * argv[] ) {
     hsd.addDefines ( defines ) ;
 
     // Add our comment saver as a comment handler in the preprocessor
-    CommentSaver cs(ci.getSourceManager()) ;
+    CommentSaver cs(ci, hsd) ;
     pp.addCommentHandler(&cs) ;
 
     PrintAttributes pa( attr_version, hsd, cs, ci, force, sim_services_flag) ;