Added const qualifiers to core MD routines

Added const qualifiers to core MD routines

Const qualifiers have been added for gmx_mtop_t and t_inputrec
for most core MD routines, except for the domdec module which will
follow later. Ideally we would also add const to rvec * and matrix,
but that doesn't work when called from C, so that will come later.
Converted rmpbc.c to C++ to enable const rvec * in mshift.cpp.

Change-Id: I4e419f82fd27374014fc57ebbd0a35f375a800ec