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

There is a new method for colvars and function, enforceNumericalDerivatives(),
which can be used in the constructor so as to enforce numerical derivatives.
It should be added to complex colvars for which we do not want to implement
numerical derivatives, or can be used at preliminary stage during CV
implementation.

I also added a check for colvar ENERGY, which cannot be done with
numerical derivatives

I overloaded fopen and fclose inside an Action in such a manner
that a list of open files is kept. This allows to flush them implicitely,
without requiring people to write an explicit flush() method.

I also upgraded the doxygen configuration files to 1.7.4 version

for icc compiler

Removed several not-necessary inclusions

I added some stricter check for deallocations of Atoms::Request
objects. I also removed the SIGMA keyword from Colvar (the right
place would be in Value). Finally, I fixed some lines which were
leading to apparent memory leakage with valgrind.

Implementation is rather general and allows one to use them not only for debugging but also for real calculation. A keyword NUMERICAL_DERIVATIVES can be used in directives such as COLVARs or FUNCTIONs, and automatically performs numerical derivatives instead of analytical ones. Moreover, I added a DUMPDERIVATIVES directive which prints on a file the derivatives of the (ARG) colvars. E.g.:
DISTANCE LABEL=C1 ATOMS=0,1 COMPONENTS
DISTANCE LABEL=C1n ATOMS=0,1 COMPONENTS NUMERICAL_DERIVATIVES
DUMPDERIVATIVES ARG=C1,C1n FILE=derivC1
will define two CVs, with the same value, but one with analytical and the other with numerical derivatives, and will write two columns on file "derivC1" with the derivatives, which can be compared for debugging.

BE CAREFUL: I did not test it with non-orthorombic cells, there may be problems in the virial components

The previous fix for AIX breaks it on linux. I now use command_argument_counts()
which apparently is the standard way

Declaration of iargc
Correct empty argument for cmd("init")

option --root was not working properly

I improved the way variable with forces acting on them are detected.
This will be useful to better implement numerical derivatives

sadic attempt of using xcode

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.

to retrieve the label and the set of dependencies

removed unused method and other clenup

Small inconsistency in usage of setValue removed

I removed some unused methods to manipulate atoms

I removed the claim that I am the only author and cleaned a bit
the introduction

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