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

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

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.

more specific in the documentation as to what precisely it is doing.

some of the English and in some cases writing new documentation.  Also sorted
a number of issues that arise because of the awkward formatting that is
Doxygen requires

This is the draft version that I prepared and that we will use as
a starting point. Still it is a bit dirty, and I will try to improve
documentation and delete unused routines