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).