Synchronicity of outputs

[alextbradley]

Currently, we do velocity solve, then update thickness, then update clock, then test for outputting, which gives a slightly asychronous result: the clock and thickness is one timestep further along than the velocity. We should output after the velocity has been updated, e.g.

    for i = (simulation.clock.n_iter+1):timestepping_params.n_iter_total 
        update_state!(model)                                               #do the velocity solve   
        check_and_output_solution(simulation)                   #output solutions if appropriate  
        check_and_output_checkpoints(simulation)             #create checkpoints if appropriate  
        if timestepping_params.step_thickness  
            update_thickness!(simulation)                               #update the thickness   
        end  
        update_clock!(simulation)                                          #update the clock  
    end

(Does this index of loop catch the final timestep?)