Small fix needed due to the fact that master branch
also calls cmd("setStopFlag") (for committor analysis)

Conflicts:
	patches/gromacs-4.6.5.diff/src/kernel/md.c

Merged a branch with a modified gromacs 4.6 patch which
allows for better load balancing when using gromacs
with GPUs.

ALMOST configuration and linking is suboptimal but I have to
work a bit more on the ALMOST side to improve it.
I added GSL because I am using them in a branch I will merge
soon.

Fixes #71

Conflicts:
	src/config/Makefile

plumed info --version
returns the branch name (or something such as v2.0 in releases)

plumed info --long-version
returns a longer description (or something such as v2.0.2 in releases)

Also updated the src/release script accordingly

Regtest crashes

Also moved
gromacs-4.6.3.diff/src/mdlib/force.c*
to
gromacs-4.6.5.diff/src/mdlib/force.c*

Now upon rewind file is moved on a backup name (bck.last.xxx).
This is to have a recover file in case of crashing while checkpointing

I merge the patch --save-originals stuff on v2.0.
I am using it a lot and I think it is stable enough to go to v2.0.
This will allow to modify gromacs patch also in that version.

Conflicts:
	patches/patch.sh

Mode is redundant since:
* read or write can be decided depending if file is IFile or OFile
* append/non-append is decided based on RESTART option

Includes restart with METAD, READ and PRINT, and --multi

Files with gz extension are transparently compressed and decompressed.

Closes #17

There is a new function that is called after every regtest, before
comparing with reference. Can be used if files produced by plumed
need further post-processing

Added diagnostic