Fixed gromacs patch

The way it was, "mdrun -plumed" was faster than
"mdrun", which sounds pretty cool but obviously was just
an artificial (slight) slowing down when using gromacs without plumed...
typo in an error message
Fixed regtests

Some non-important error (missing links) probably remaining from the
reorganization of tests.
Fix in WTE with multiple processors per replica
Small optimization in neighborlist building

Avoid sqrt in inner loop.
Added CHANGES/

I added a directory CHANGES where we can add short description
of changes among versions. I use a separate file for each branch
(v2.0.txt now, then we can add v2.1.txt in the master branch)
so that it will allow merging from old branches to new branches
as usual.
CamShift and replica-averaging
- Clean up
- Units conversion from plumed to almost
- Rename of the Class
more options
removed a repeated if
remove multi_sim_comm from CLToolMain
Bug fix in switching function

D_MAX was not correctly interpreted.
A few stuff for Hamiltonian replica exchange

I use them from my Hamiltonian Replica Exchange implementation in
gromacs. They are harmless, so I include them already in plumed release.
This will allow me to include HREX just with a modified gromacs patch.
CS2Back first piece of documentation
copy of the intersim communicator here instead that in the patch
as Giovanni suggested
Merge branch 'CamShift' into v2.0
Optimized building new request list
Bug fix

Was introduced with CamShift (my mistake in suggesting a hack to Carlo).

In fact, because of the way stopwatches are implemented, it is not
possible to call plumed.cmd recursively. I made a quick fix (the
right fix would be to adjust stopwatches)
Modified use of neighbor list in COORDINATION

It solves a known problem with the calculation
of acceptance in replica exchange with COORDINATION
and NLIST.

Notice that it changes the behavior of neighbor list
in the first two steps of a simulation. Previously,
during those steps full pair list was used. Now,
first step is equivalent to any other step
multiple of NL_STRIDE. Because of this, I updated
a couple of regtests.
Added regtest for neighborlists

This is to probe correctness with replica exchange