cc: @valsson

I went through cppcheck warnings (style) and fixes those I understood.
Mostly issues related to scope of variables.

Notice that almost all files were updated with the astyle commit
2813d759

Year in header is here updated to 2017

This is a huge commit, applying indentation to the whole
code. Notice that this commit is made on master branch
after having merged with -s ours from branch v2.3

See #215

This is a huge commit, applying indentation to the whole
code.

See #215

It is now possible to specify a different link cell cutoff for the
third bodies.  In addition, the way that connectivity is determined
in adjacency matrix actions works better given that we can now
operate with non-contact matrix contact matrices.  Also added some
cutoff stuff to HistogramBead.  This is currently not used in many
places

(cherry picked from commit b6ea36c1)

For reasons lost in the mists of time to set histogram beads you
had to pass an empty string.  This is no longer necessary so I
removed it in order to make this class easier to use

CAVITY multicolvar allows you to calculate all the usual
multicolvar things but for those atoms that are in a
particular part of the box that is determined based on
the positions of four atoms.

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

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.

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

I used cppcheck --enable=all.

I replaced all the "using namespace PLMD" statements with explicit
namespace PLMD{ …… }. This is more clear and simplify the syntax for
defining operators

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

I have tried to make this multiColvar more flexible.  In essence
the average value of the CV is calculated in a region of fixed volume.
This volume can be specified in terms of the cell box and I am planning
to add other ways of specifying the volume presently.  The old version
of this particular multicolvar thing was actually not working so as well
as being a rework this is a fix

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

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.

the WITHIN keyword range as well as the number of colvars within a given range.

I tried to remove a lot of includes using forward
declarations