Added virtual method update() to Action

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).