Fix and clean up handling of some linking

Fix and clean up handling of some linking

Split GMX_EXTRA_LIBRARIES to several lists, depending on the intended
use of those libraries.  Some of these also need to be linked by code
other than libgromacs, either because they are required by the public
headers (mostly -lm), or because also code outside libgromacs directly
references those libraries (e.g., MPI).

Should fix #2087.

Change-Id: Ie0e211b8f77a932ccd63017ee0743b78361624c4