Slice the onions in 1/4-inch thick. In a heavy bottom pot, slowly simmer the onions in the olive oil over medium-high heat for a few minutes until softening. Add all the remaining onion confit ingredients. Bring to steamy simmer. Reduce heat and cover with a parchment paper lid that has a 2-inch hole in the center to allow the steam to escape but protect it so that it can cook low and slow. Press the parchment paper down to touch and cover the onion mixture. Place the covered pan into a 250 degree F oven and bake for 2 to 3 hours or until the onions have softened and the liquids have reduced to a sticky gravy that clings to the onions.
Slice ends off the tomatoes. Cut the tomato through into 2 to 3 slices. In a mixing bowl mix the tomatoes, thyme, garlic, olive oil, salt and pepper. Gently toss to coat the tomatoes. Place on sheet pan and cook at 250 degrees F for 2 to 3 hours until the tomatoes are concentrated and dehydrated. (The onions and the tomatoes can cook in the oven at the same time.)
Raise the oven temperature to 450 degrees F.
Stretch or roll the dough to about 10 to 12 inches. Place a piece of dough on a pizza paddle or baking sheet that is sprinkled with cornmeal. Oil the edges of the dough and top it with Fontina, 1/2 of the onion confit, the sausage slices, tomatoes and top with mozzarella. Bake until golden brown. Top with parsley and serve hot.
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