Patch for Native Client builds.

This patch contains the source changes necessary to compile Gromacs
for Native Client.  Patch is based on original work by Ivan Krasin,
additional changes from Joseph Coffland.
Also included are a few compiler warning fixes and a minor FAHCORE
tweak.

Change-Id: I085c52ff1d8e45ec8ffb8c56f5877313d6225bb2
Checkpointing fix for Native Client

Native Client doesn't allow file renames.  We can over-write output
files, however.  For checkpoints, live dangerously and skip backups.
The alternate would be to use an in-memory file system, but then we're
still screwed if the program gets killed partway through writing the
on-disk version.  Other alternates:  keep all checkpoints.

Change-Id: I952ee6436e69f015633a150f94fca65c7271c6bb
Merge release-4-6 into master

Conflicts:
	src/gromacs/gmxlib/checkpoint.c
	src/kernel/genalg.c
	src/programs/mdrun/md.c
             (moved change to trajectory_writing.c)

Change-Id: Ia9c8722c7fb80d48d8e40cec2af0cb93dc7e468e