Remove some backwards-compatibility glue for Jenkins

- GMX_CPU_ACCELERATION has not been used in a long time.
- The Documentation job should now be easy to update to use
  'make check-source' instead of 'make doc-check'.  There have been
  various bumps to the regression tests that already make Jenkins vote
  -1 for all changes older than the introduction of 'check-source',
  so an additional negative vote from the Documentation job should not
  matter.

Change-Id: Ic9908b2cdb56b43823c4f2c5e53294688f1af89d