Currently it is only possible to trigger focus stacking from the ML menu. Please allow focus stacking to be triggered from a remote in the same way exposure bracketing is triggered. This helps avoid camera shake and allows automated focus stacking using a motion control rig (e.g. Kessler Slider / Second Shooter).
Also looking forward to this. If anyone could guide me, I would be glad to make module/script to make it work :) . Just don't know where to begin.
@Pedr
Although my interests are directed at landscape focus stacking, which is slightly more complicated than macro focus stacking, I have 'successfully' demonstrated auto focus stacking using Lua scripting, ie triggering from any button.
Unfortunately, some of the core ML and Lua coding needs fixing for the auto focus bracketing to fully work (my current script is not stable), as, at the moment I can't drive the lens both ways and you can trigger 'soft end' errors. Once this gets fixed, I'll release my auto focus stacker script.
My manual focus stacking experiments with Lua are here: http://www.magiclantern.fm/forum/index.php?topic=16659.msg162352#msg162352