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

Without STORE_GRIDS it is necessary to flush the grid file,
otherwise it might stay empty for the entire simulation

When not RESTARTing:
file is backed up if existing.
  with STORE_GRIDS, file grows during simulation
  without STORE_GRIDS, file is replaced every time grid is rewritten

When RESTARTing:
  with STORE_GRIDS, file is appended and grows during simulation
  without STORE_GRIDS, file is replaced every time grid is rewritten

This hopefully fixes #34
  

It is possible to print html links to failed tests.
I am setting a nightly build and want to publish online
regtests results

One can know use e.g.
./configure mpi.linux.icc
to directly select the configuration and avoid interactive
choice. Better for building from script

Relevant when using a huge number of restraints

Running a LJ in LAMMPS (no charges) was crashing

cmd("useNaturalUnits") was erroneously crashing

Removed many scans of the output buffer by keeping trace of buffer length.
Time needed to write a long line with a sequence of file.printf() is
now linear with line length. Before it was quatradic, causing problems
especially when logging huge atom lists at startup.

I added a check that disables this combination which can
be problematic. I had to also update a regtest

You can now read in groups with names other than GROUPA, GROUPB and
GROUPC.  Also output of the atoms in groups is neater.  Lastly I realized that I
had accidentally added some crap to regtest/multicovar/rt45 - I have
now deleted this.

* Better algorithm for int powers
* Simplification when 2*N=M (which is the usual case)

The note "shell only version ..." now goes to
stderr instead of stdout. This is better, because some tool
might produce a meaningful stdout and that should be the
same when using "plumed xxx" and "plumed-xxx"

Now all the scripts in /scripts are mapped to executable scripts
in the form "plumed-xxx" (similarly to "plumed-patch"). Allows to use
those shell tools in a cross-compile environment (e.g.
to use plumed-mklib on the login node when plumed is compiled
for compute node)

I also changed a regtest as a check

There was a potential bug when stripping blanks from short strings (1 char)

This is a quick fix to avoid regtest failures. The real bug
is the fact that wrapatoms is not read on input in simplemd,
and should be fixed (see #30)

Here you can use regex to refer to argument in a list
For example in
t1: TORSION ATOMS=5,7,9,15
t2: TORSION ATOMS=7,9,15,17
d1: DISTANCE ATOMS=7,17 COMPONENTS
PRINT ARG=(d1.[xy]|t[0-9]) STRIDE=100 FILE=colvar FMT=%8.4f

with this keyword you can limit the range of sigma when using the
adaptive Gaussian scheme.

With this fix plumed crashed when using ADAPTIVE=DIFF and replica
exchange.