I fixed the usage of stopflag in driver so that it is clearer
that the program stops at the end of the present step and not
at the beginning of the following. This is obviously equivalent,
but shows that scope of the flag can be reduced to be defined
at the inner of the MD loop.

Even if this is not a bux fix, I consider it as paired with fix #47
and I merge it to v2.0

(should be checked by GT)

This test shows a problem in reweighting (discussed in #48).
In particular, histoA and histoB in this regtest should not
come out identical as they do.

I think this is more coherent with other cmd() calls.

The interface to set replica communicator from fortran was missing.

It just prints a meaningful error.

file the residues they use.

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.