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

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

Documentation is still a bit poor. I used it to replace
the Log implementation and also for in the GenericPrint class.
In the log, this implies a small change (FIELDS line is
written in also in the log).

I tried to make everything so that regtests are not affected. Only,
change, now the rt17 (using _ROTATE) works correctly, writing
field names as they are updated.

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.

no instances of this class are created anywhere

(merged from gat2-reorder branch)

fixed buggy loop in Keywords remove

Sorted out html alignment for keywords stuff.

I think that the compiler is doing something wrong here...
Still I fixed the error (uninitialized buffer) so as to
only detect real ones.

already implemented somewhere else, but I am using it
for debugging.

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.

Removed several not-necessary inclusions

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