Flux and source Jacobians w/r/t conservative variables

[cwentland0]

Right now, all of the flux and source classes provide Jacobians with respect to the primitive variables only, which is fine for dual time-stepping (dual_time = True), but is not okay for normal time integration (dual_time = False). The current solution is to simply right multiply the primitive flux and source Jacobians by Gamma inverse, but this is not exact in the discrete setting. Thus, routines for calculating the flux and source Jacobians with respect to the conservative variables need to be added, and calc_res_jacob() needs to be updated accordingly.