Fix HTML links that contain file extensions

- Consider '-' and '_' as part of a word when replacing links, so that
  convert-tpr and make_ndx are considered single words, and the
  extensions there are not converted into links.
- Do links.dat replacement before program links, so that the URL in the
  above program name links is not processed.

Change-Id: I0ce204d3adedc56e57c1e1cd150a63d21c442eab