Documentation and cleanup of PISM.util.  Added new PISM.vec module. Removed PISM.toproczero.

This will break PISM python code outside of the PISM repository:

PISM.toproczero module was deleted (contents migrated to PISM.vec)

Vec related objects in PISM.util, including PISM.util.Access were moved to PISM.vec.