The new multicolvar measures the inplanedistance i.e. the
distane from a plane defined by a vector connecting two atoms.
The new refernce distance measures the dot product distance
between two points

To do this I had to make requestArguments in ActionWithArguments
a const method is this a problem?

The reference module means that you can use different types of metric when
calculating the separation between the instantaneous position and a reference
configuration.

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

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

I want to reuse stuff from these classes to do some other things and
I needed to make a few small changes to make the new things work.

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.

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

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

As a general rule, when one adds a file he should run
./header.sh
This will add the LGPL header to all the sources. 

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.