This new multicolvar calculated using the XDistances class.  This
class is registered three times for the commands XDISTANCES, YDISTANCES
and ZDISTANCES.  The changes to ActionRegister.h are what allows me
to do this

MultiColvarFunction allows you to calculate thing like the average coordination
number for the atoms an sphere centred on a particular atom.  If crystallization
is installed you can also use it to calculate things like the local q4 parameter.

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

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.

These changes allow more flexility when we use functions of the set
of quantities calculated by MultiColvar.

Now all multicolvars can have a central atom position and can be used in
multicolvar functions.  This makes the code a bit clearer.  Also secondarystructure
variables are now faster as much copying of derivatives is removed.

This makes these two classes slightly simpler.  It also allows one to
use MultiColvarFunctions on MultiColvarFunctions.  We can thus do things
like the value of the dot product of the q4 vector on a atom with the
q4 vectors on the atoms in the first coordination sphere averaged over a
subregion of the simulation box.

Mostly unused variables

It is very difficult to write a generic description of the GROUP keyword
so I changed the documentation so that you have to write documentation for
GROUP in the MultiColvar you are implementing.  So now DISTANCES contains
the keys.add(atoms-1,"GROUP") bussiness, this is no longer in MultiColvar

I have greatly simplified the hierarchy of classes that inherit from Vessel.
Furthermore, I have re-used much of the parsing functionality in Action so as
to make adding a Vessel more like adding an Action. All the changes in regtests are
just because of changes of the names in the header line.

In addition I added functionality so that multicolvar can pretend to be colvars
Multicolvars have value that are always labelled as label.something.
However, in AlphaRMSD etc the default is to calculate the number of
RMSDs that is less than a certain target value.  Furthermore, in the
manual these MultiColvars are listed as colvars.  The multicolvar functionality
inside alpharmsd being a feature for "advanced users".  Hence, to avoid confusion
I added something so that by default the value in alpharmsd etc is just
label.

This is an attempt to make it easier to re-use ActionWithVessel for things other than
MultiColvar. There are multiple ways to do a neighbor list and so I felt this functionality
should be separated somewhat.  In addition the way I had implemented the neighbor list for
multicolvar meant that the list was being updated one step later than it should have been.
Also did some tidying of the multicolvar and vessel code

The multicolvar way of doing DHENERGY is particularly useful if you want
to calculate multiple instances of the DHENERGY with different parameters.
By using the multicolvar you can avoid the recalculation of the distances
for each different parameter set. You can also use the multicolvar to calculate
COORDINATION (LESS_THAN) and the DHENERGY for two groups of atoms at the same time

In addition I have made all vessel classes have their own
separate header and cpp files. I have also renamed what
was ActionWithDistribution to ActionWithVessel

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

doing the same thing.  Also sorted some documentation for
these keywords

with their regtests.  Have moved these to my own separate development
branches.

did distributionGradient and distributionCVdens properly.  Before I had
forgot the cell perioidicty and so these functions were calculated wrong.
Had to change some regtests as the colvars they were testing were
implemented wrongly

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.

We now basically ignore everything that makes a small contribution and focus on only
the larger contributions to the final function

fields and the various functions of the distribution of whatever the collective
variables are

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

is an overlap integral between the current field and some reference
field ( this can be a sum of fields visited at previous times ala metadynamics ).
To test the derivatives of the field I changed calculateNumericalDerivatives
this routine can now be passed an ActionWithValue so that you can differentiate
objects where something other than a value is passed between Actions.  Currently
only histogram style field cvs are implemented.
Wrote documentation for FIELD keyword and for MOMENT keyword.  Also
rethought numbered keywords and so changed the keywords class a little bit
Changed number of decimal places in tests so that they worked on other
computers.  Also made test 23 much less expensive
Fixed a very persisent bug in field cvs - horay!!!

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

normal plural surely