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

Patch adapted from Toni Giorgino.

use "plumed gentemplate --list" to print list of templates
use "plumed gentemplate --include-optional --action PIPPO" to include
 optional keywords for directive PIPPO

Added a tool for generating template versions of the various collective
variables.  This involved changing the secondary structure variables
work (by default you now do LESS_THAN).  In addition, plumed now understands
that atoms can be specified in multiple ways sometimes.

Also changed the developer manual so as to make it easier to find the
tutorials

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.

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.

I tried to remove a lot of includes using forward
declarations

action in html.

Fixed it so that the output of html also works for keywords that don't take
any input (for instance SetupUnits)

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).

It takes care of dynamic loading, and unload libraries when plumedMain
is destroyed. This allows for a complete memory cleanup at the
end of execution.

I removed several (hopefully) not needed include

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