Manually sort some includes in src/gromacs

Sort manually includes in files where there are #ifdefs within the
include statements and the automatic sorter does not do a good job
because of this.

This commit does this for files found in src/gromacs/.  Files from other
locations will be done in a separate change if there are any.

Fix nbnxn_cuda.h to work without requiring code to include
nbnxn_pairlist.h first.

Change-Id: I26fa1a28ea9094a62c826d8ee65ddabac345da68