Misc. gmxpre.h-related changes

Related to selection parser generated files:
- Add gmxpre.h to the generated selection parser files. parser.cpp and
  parser.h are now generated with a newer bison version, since that is
  what I happened to have available.
- Minor improvements to the regeneration script.

Related to the doc-check target:
- Make the doc-check target happy again by removing a check that is not
  valid in the current state.  Minor clean-up in the script.
- Add a checker for the presence of gmxpre.h in all files where it is
  expected to appear.
- Move one suppression from config.h to gmxpre.h, since that is where
  the code now is.
- Use consistent #include "config.h" in vec.h and remove blanket
  suppression for that issue in doc-check.

Change-Id: I1e803ef000c5b2c685532c9e47df534ef5b263bc