I used cppcheck --enable=all.

This avoids complains from make doc

Since the SetupMolInfo action is used by other ones, I left it
in core/. It is however registered in setup/, so that it can be excluded
disabling that module. Moreover, I added a method so as to remove
a friend statement in PlumedMain

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

This will allow to parse units also in places different from SetupUnits.
I also modified the Units class in such a manner that data is private
and access is safer. This required to change all around accesses
to its components.

Curly brackets {} should be used instead of parenthesis () to delimit input
parameters. This will allow to use parenthesis in matheval.

Regtests and documentation have been updated accordingly - I hope there not
inconsistencies around!

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.

was calculated wrong in this class, oops...).  Added alignment of strands for
beta sheets when calculated using RMSD proper.

User doc should not use the Doxygen "/**" otherwise it appears
also in the developer manual

Also got rid of the stuff on beta sheet between chains as I wasn't
sure how to make it work

in terms of the residues for the chains for which one wishes to calculate the distances
from the alpha helical secondary structure.  For these reasons I had to adjust the PDB
parser so that it reads in atom symbol, resdiue and chainID data.  I then I have an
ActionSetup class (MolInfo) that can read and store the data on the various chains inside the
pdb file.  I have that you can calculate the distances from the secondary structure using either
DRMSD (like plumed 1.0) or using Davide's RMSD class.  This required a very small change to Davide's
RMSD class.