[makedoc]

For DISTANCE, ANGLE, TORSION and PUCKERING,
I implemented something similar to GYR, where atoms coordinates
are first made whole, then the virial is computed assuming them whole.

Notice that modified coordinates are the local ones, so that the
change does not impact other actions.

Moreover, this required fixing numerical errors in a couple of regtests

to include the description of the current shortcut
for dihedral angles (@phi, @psi, @omega, @chi1)

@ sign is now used within plumed to specify special groups of
atoms or special colvars whose labels are created by plumed and
not by a user

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

Namespaces are used now in bias/colvar/function/cltools

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

Periodicities of values are stored as strings inside Values.
These strings are output as constant fields inside the colvar and
hills files.  In addition the fact that we now use strings means that
when you have a function and you have to specify its periodicity you can
use PERIOD=-1.5pi,1.5pi or some other thing like that

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

but I do not have it on my cluster and I was lazy.

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.

Due to default values in flag, it makes no sense to have
a flag with default value "true". I thus removed PBC from
the keywords for colvars. Now they are default on and can only be
switched off (with NOPBC).

Many checks on size() transformed in checks on empty()
(suggested by cppcheck)

independent of ActionWithValue.  That is to say there is no
longer a reference to an ActionWithValue object inside Value
objects.  I also changed many of the names of routines inside
ActionWithValue. This is to try and make this class as transparent
as possible to the end user.  There is also extensive documentation
for ActionWithValue

the fact that one position is returned by this routine

have input replaced by atoms and objects that don't appear in the manual
appear as nohtml rather than modifier.  Also got rid of automatic size
checking of vectors in parseVector when the vector passed to the parse
routine has zero size.

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

See TORSION manual.

I tried to keep the tools to compute them separate from the
colvar implementation, so that it will be possible to use them
for other colvars.  For torsion still I am using numerical derivatives!
This clearly has to be fixed.

I debugged them against plumed1. Also, for angle, I checked the
derivatives comparing with the numerical ones and I still
have the usual problem with some off-diagonal contribution to
cell derivatives when applying pbc. There might be some hidden
bug there to be fixed...