[makedoc]

closes #158

added PERIODIC=NO in the example because this keyword is compulsory.

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

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.

to singular objects but that had names that were plural.  This
is resolved by this commit.

for specific tasks.  To reserve a keyword use keys.reserve() and to
then use it later use keys.user().  Currently the reserved keywords
are ARG and PERIODIC.

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

that I (Gareth) made and have now resolved

various actions below.

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

so that aix compiler does not complain about an empty file

Added full documentation for all directives.
I also made some small fix to manuals

Implementation of periodicity as we discussed at the meeting.
In the constructor of a collective variable or function is it possible
to declare, for each value, if it is periodic or not. E.g., torsions
will be periodic, distances not. The difference between two values
(hypothetically, a stored value and the present one) can than
be computed automatically using a Value::difference() method.
If difference() is called for undeclared values, an error is raised.
Thus, functions of unpredictable periodicity (e.g. MATHEVAL) should
allow the user to specify the periodicity (or the non-periodicity)
in the input line.
See how I implemented the setting of periodicity in the available
Colvars. The syntax is a bit baroque (I will probably simplify it),
but it seems to work.

I also added a check on the fact that two labels can not be equal.

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