For the focaccia dough: Put all your ingredients in the bread machine, in the order your bread machine suggests. Select the dough cycle. At the end of the cycle, dump the dough on a well floured board, and shape it into a circle. Pat it out until it's about 12 inches wide. Brush the pizza with olive oil, cover with plastic wrap, and let it rise for thirty minutes.
To assemble the pizza: Heat the pizza stone in the oven for thirty minutes.
Mix together the cream cheese and creme fraiche and spread it all over the pizza. Sprinkle on the bacon and onion, brush the crust edges with olive oil, and bake the pizza for 15 minutes. Remove the pizza from the oven and brush the pizza with more oil. Then, add the pepper jack cheese and jalapenos and bake for five more minutes.