This fixes an issue on periodicity of values.

Now all the values are brought within their periodic boundaries.

Duh!  That was stupid.  Change to Value is to add setDerivative
method

This functionality is not complete.  In multicolvar this is
done correctly.  However, for normal colvars and the like
derivatives are still calculated even when they are not required

I set it to 2 instead of 2.0, so that it will not be necessary
to update it

Now, for consistency, the time units of SIGMA in METAD for the
ADAPTIVE=DIFF scheme is in timesteps to be consistent with the rest of
the program. Documentation, printout and regtests are done.

Speeds up RMSD quite a bit with -DNDEBUG

If you want to but a plumed_assert in a loop you should now use
plumed_dbg_assert / plumed_dbg_massert.  This will not be included
in the code if you compile with -DNDEBUG

The guard "ifndef/define" has been updated so as to also include the
module name. This is important as it will allow files with the same name
to be used in different directories. Modification was done automatically
using header.sh - just run it routinely to keep names consistent

All the source code have been moved into subdirectories of src/
Some of these subdirectories are treated in a special manner:
src/wrapper contains the wrappers for MD codes
src/main contains the main.cpp file
src/config contains files generated without compilation,
  just based on configuration info
src/lib is the place where executables and libraries are put
  at the end
src/cltools contains the command line tools
src/tools contains plumed tools (reusable classes)
src/basic contains PlumedMain, Action hierarchy and other basic stuff
src/multicolvar contains MultiColvar stuff
src/imd is the interactive MD (still not totally portable).

Notice that, to allow easy inclusion of .h files from other modules,
I link all the directories in src/ into module directory. In this
way it is possible e.g. to write #include "config/PlumedConfig.h"

See src/README and src/basic/Makefile to understand how inter-module
dependencies are set

Periodicities of values are stored as strings inside Values.
These strings are output as constant fields inside the colvar and
hills files.  In addition the fact that we now use strings means that
when you have a function and you have to specify its periodicity you can
use PERIOD=-1.5pi,1.5pi or some other thing like that

modular.  It is now easier to remove features of multicolvar and
to add new multicolvar features.  In addition the functionality of
multicolvar is now more reusable.

as suggested by Gareth

I added a PEOPLE file containing list of authors and a script
(src/header.sh) which applies the Licence to all the source files.

It can be applies multiple times (it automatically deletes the present header
and replace it with the new one). Thus, to change the header, edit header.sh
and execute it.

This is the adaptive hills scheme that is called in the metadynamics just by using
ADAPTIVE=GEOM SIGMA=0.1   (only one sigma, in this case has units of distance)
or
ADAPTIVE=DIFF SIGMA=10.   (only one sigma, in this case has units of decay time)

the output in HILLS changes accordingly and presents MV (multivariate) that stands
for a band-representation of the cholesky-decomposed sigma^2
(in which at the beginning you have the diagonal terms that should give you an idea
of how wide are the hills).

structure variables.  To do this I had to write a proper constructor for Value
when they are created outside ActionWithValue in ActionWithDistribution. The lack of a proper
constructor was causing problems with strands cutoff for antibetarmsd. This was a stupid bug

I think this could allow us eliminating the DEVELDOC
preprocessor.

The point in CV space can be specified using a pdb file, hence the changes
to Action, Value, etc - all these changes are all so that you can calculate CVs from a
pdb input file.  Whilst I was messing about I noticed a potential problem with
natural units and input pdb files.  As we are in natural units there is no
way of knowing how to convert the pdb from angstroms (unit in pdb)
to the natural length unit.  For these reasons I assume that when one is in
natural units pdb input files are also in natural units, this required changes
in ColvarRMSD and my new ColvarTarget routine as well as a small change in Atom.h.

Added funcitonality so that one can restart field cv calculations
Added field cvs for contact maps

I tried to remove a lot of includes using forward
declarations

Many checks on size() transformed in checks on empty()
(suggested by cppcheck)

calculate all the collective variables so that the field can be calculated
Adjusted apply so we can use all colvars in fields
Added routines to pass periodicity and domain to values

the way I was using it was inefficient.  Also added add function to Value so that I can
accumulate quantities in values rather than just setting them
Made it possible to accumulate more than a single quantity in ActionWithDistribution.
This extends the range of mathematical functions one can work with using this routine.
I have also made the mpi in this routine more efficient - com.Sum is now only called
once per step
Added product and quotient rules to make for easy manipulation of derivatives

You can turn on the naive way to parallelize the code or do it
yourself in your own routines.  Also added regtests for this
functionality

Conflicts:

	src/ActionWithDistribution.cpp

added stuff to check that the value was set and actually
made addDerivatives addDerivatives rather than set them

Changed the way values work so that the ActionWIthVaule pointer is
inside

independent of ActionWithValue.  That is to say there is no
longer a reference to an ActionWithValue object inside Value
objects.  I also changed many of the names of routines inside
ActionWithValue. This is to try and make this class as transparent
as possible to the end user.  There is also extensive documentation
for ActionWithValue

I moved the difference routine inline. This enforces to include Tools.h into Value.h, but give much better
performances. I also changed the order in which the conditions are evaluated, leaving the less likely at the end.