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

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

so that we can generate fields.  Also fixed various bugs in multicolvar
gradients.  There is one recurring bug and I cannot work out what I am
doing wrong.  The off diagonal elements of the stress tensor are wrong
when you do GRADIENTS and SUBCELLS.

now use Giovanni style switching function input everywhere

Switching function works also corrected regtests.