Small change in the mani flow. Now, after the backward loop to apply
forces, there is another forward loop calling "update()". update() should
be used to dump/analyse data, and/or to modify a biasing potential
(e.g. in metadynamics or tamd). Also, since it is called after full
calculation, analysis tools could access to more quantities (e.g.: forces
on a specific CV have been already computed and could be dumped).

The rationale is to avoid duplicate lines in the COLVAR file when
an exchange is attempted in replica exchange. Still, this solution is not
totally satisfactory. I think we should add another virtual method
(maybe update()) to be used for printing, accumulating statistics,
and e.g. for updating HILLS.

This option allows to regularly change the argument printed by PRINT.
Notice that it does not write the correct header, and it is here
ONLY for trying the requestArguments() feature.
When we will have a real function/bias using that feature,
we can remove this crazy option

I try to clean up a bit the file names. All the .cpp corresponding
to input directives are now prefixed with the category of the
directive (it was already like this for Colvar*, Bias* and Function*)

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

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.

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