Other fixes to gromacs.m4
Using new versioning system inside Gromacs.cpp
Added support for Gromacs 5.x

Everything seems to work fine. However I need to do some testing.
 * Added ProgramContext class to let gromacs know where files are
 * Added support fore new version inside gromacs.m4
 * Put everything that must be declared because of internal APIs inside
   namespace gmx_legacy. I know that using internal APIs is not a good
   idea, but I would have to rewrite lots of things and also I would
   have to use 'its' behaviour, and I don't like it.
 * Fixed some gromacs version checks