MMS test of time integration methods

o RK3SSP and RK4 methods weren't saving their final result
  to the output, which reduced RK4 to 3rd order, and RK3 to 1st order.
  Now produce expected convergence rate

o Karniadakis scheme now converges at 2nd order. Needed to change
  how the first timestep is handled, so now an Euler method is used
  to reconstruct previous timesteps. This has an error O(dt^2).