Write out time step #0, too

(1) Determine distance from patch properly (also in general polygon cases)
(2) Move refine()
(3) Rewrite the logic of the patch (allow it to be a polygon)

During the first fixed point iteration, velocityIterate and the old
velocity are identical except for the new BC: velocityIterate has
already had them imposed.

To simplify the control flow, kill v completely.

Note that since we always make two fixed point iterations and this issue
only occurs during the first step, this change only affects
computational results as (a reduction of) noise