Reordered code and comments at end of gmxtest.pl

* Moved XML-writing setup out of the way, so it is easier
  to see what's going on at the end of gmxtest.pl, because
  there's bugs to fix.
* Moved comment about setup_vars back next to where its call
  is triggered.

Change-Id: Ibb9f3ca25639752b0a171d5446f50beb0beefdd3