I added the possibility to avoid copy of atom coordinates for specific
Actions. Since WHOLEMOLECULES is accessing to atoms in a special manner,
it is now faster.

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

This modification ensures that multicolvar uses less memory and makes
it a tiny bit faster

For a number of complex multicolvars eg. Local_q4 it is useful
to store the quantities calculated in one multicolvar and to use them later.
I had written functionality for this in a somewhat ad hoc manner intially and
as such there was much duplication of code and non uniformity in implications.
This resolves these issues.  Data is now stored more consistently and it is possible
to use a low memory version of this functionality at all times.

This routine no longer made sense in the code

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.

Conflicts:
	src/config/Config.h
	user-doc/Doxyfile

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)