Clean up inputrec reading

In old code, there was no way to reset the state of the string buffers
that were used in parsing the inputrec from .mdp files. This was a
problem for test executables trying to parse more than one such
file. New code still doesn't permit more than one .mdp file to be
parsed at a time, but at least we can clean up and parse another one
from a fresh state.

Got rid of some useless #defines.

Change-Id: If3d72ba68e0addef18c9cf132025958995e7e2ee
Define MPI_INT64_T if not defined by mpi

Change-Id: Ie3332ce85a5ef538d57b272ebe3e4326fb7a31ff
This patch moves preprocessing headers to gmxpreprocess

In the move to depopulate the legacyheaders directory
http://redmine.gromacs.org/issues/1415 this is a small
contribution.

Change-Id: I209f6e5a1e76f2d3ea072f66eca9ae1f59bc0d42
Fix, simplify and test XTC writing

The old implementation had various sins, including repeating setup and
leaking natoms_xtc rvecs of memory per step writing xtc-grps when they
are a subset of the whole system. Cleaned lots of things up.

Added integration-style tests for XTC writing.

Added more grompp -n support to integration-style tests, though not
all of it is actually used by this patch.

Also added a pragma to work around a curious warning by ICC 12 on
Windows.

Fixes #1423

Change-Id: I3a75f890f21e4a87be62bcf877eb5c471670286d