Updated user manual plumed -> PLUMED

To be consistent with the paper, plumed is always capital letters.
I also changed 2.0 -> 2 and 1.0 -> 1 for sake of generality
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
Added reference to accepted paper
Added reference to paper in manual
Fixed PLUMED_KERNEL variable in modulefile
Secondary structures CVs were not writing correctly in the log
file the residues they use.
Merge remote-tracking branch 'origin/v2.0' into v2.0
Merge branch 'v2.0'
Merge commit '6d826e8ac6c005a575742349ded84be189775fe8'

This will simplify merging between branches with changes in
the gromacs patch