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.

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

should not call the Action::registerKeyword stuff.

Indeed, since we stay on multiple inheritance, Action the keywords
should be added by the daughter classes

Added keyword registering functions to Action, ActionWithValue, ActionWithArguments and ActionSetup.
Also added variables so that the keyword list can be passed to the Actions

(merged from gat2-reorder branch)

Added keyword registering to all the action classes listed below

(merged from gat2-reorder branch)

Added register keywords functions to all the classes below
(merged from gat2-reorder branch)

Fixed the registerKeywords routines in the committed subroutines

Made sure colvar is adding keywords for numerical derivatives

Oops... genericDebug should register keywords for action pilot.  It does now

Added keyword registering for moving restraint

Added keyword registering for NATURAL keyword

COMPONENTS should have been registered as a flag and not an optional oops

I tried to also add error messages, at least when I knew the meaning
of the assertion...

Basically I replaced all objects included in other objects with references, so as
to eliminate the need to include the corresponding header file. In this manner the
entanglement of compilation is greatly reduced.
Forward class declaration is now used everywhere excepted for:
* cases where it is impossible due to inline functions
  (for efficiency or because they are templates)
* cases where it is impossible due to inheritance
* small objects of fixed size such as Vector/Tensor/AtomNumber/Units/Pbc
* classes of std:: namespace (it is not possible to forward-declare them).

I replaced many of the "low level" assertions, trying to add messages here and there.
Still, this is mostly for developers: errors in the input file should get better reports.

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