Topas v5 and v6 include a number of options for including stacking faults using a supercell approach. In particular, v6 contains significant speed ups. These include use of an intelligeng peak buffer; a process which allow the rapid averaging of hundreds of individual supercells; a smoothing technique to approximate supercells 10-20 times larger than those used; and efficient algorithms for generating stacking sequences. There's a speed gain of several thousand over a conventional Rietveld approach. The language for describing supercells is deliberately similar to that used in DIFFaX.

Details are in the manual and in the the publications below. There's also an online tutorial featuring some of the examples from the Topas User Meeting in Bari. It is available here. You'll be able to get simple one or two parameter fits to data like:

You might also be interested in the following papers:

Coelho, Alan A., J. S. O. Evans, and J. W. Lewis. “Averaging the intensity of many-layered structures for accurate stacking-fault analysis using Rietveld refinement.” Journal of Applied Crystallography 49, no. 5 (2016): 1740-1749. doi

Ainsworth, Chris M., James W. Lewis, Chun-Hai Wang, Alan A. Coelho, Hannah E. Johnston, Helen EA Brand, and John SO Evans. “3D Transition Metal Ordering and Rietveld Stacking Fault Quantification in the New Oxychalcogenides La2O2Cu2–4 x Cd2 x Se2.” Chemistry of Materials 28, no. 9 (2016): 3184-3195.Link

Bette, Sebastian, Robert E. Dinnebier, and Daniela Freyer. “Structure solution and refinement of stacking-faulted NiCl (OH).” Journal of Applied Crystallography 48, no. 6 (2015).Link