Added --save-originals to patch

I added a new mode to store patches. If one saves them with
--save-originals (instead of -s) what happens is that
/patches/codename.diff
will be a directory. Instead of storing diff files there,
we will store original/modified pairs.

When patching, if a directory is found in
/patches/codename.diff
the diff are computed and then reapplied on the actual files.

The only change is that the diff is not stored but re-computed on-the-fly.
This has a completely equivalent effect of the original way.
E.g., one can patch two slightly different versions
of an MD code with the same patch.

However, it has the advantage that stored files are more friendly.
E.g., one could directly edit them. Also the git-merge of two
different patches should work better now.
Storing gromacs 4.6.3 diff with original files
Merge branch 'v2.0-save-originals' into v2.0-hrex-save-originals
Merged patch into gromacs-4.6.3

As of this commit, to patch with Hamiltonian replica exchange
just use the gromacs-4.6.3 patch

This will simplify keeping up to date with upstream changes in the patch.
Improved hrex patch

This now allows to activate hrex from the command line:
mdrun -hrex
Fixed acceptand for HREX and NPT

The contribution from gromacs (DeltaP*DeltaV) should not
be counted with hrex. Indeed, this term is already included
in the foreign energy calculation.