How to Make It
In a large bowl, mix the yeast with the water and sugar and let stand until foamy, about 5 minutes. Add the olive oil, thyme and salt. Add 2 cups of the flour and stir until a very soft, wet dough forms. Turn the dough out onto a lightly floured work surface and knead, working in about 1/3 cup more flour, until the dough is soft and silky. Shape into a ball and put in a large, oiled bowl. Cover and let rise until doubled in bulk, about 1 hour at room temperature or overnight in the refrigerator.
Preheat the oven to 450°. Oil 2 large baking sheets. Heat the olive oil in a large skillet. Add the onions and stir to coat with the oil. Cover and cook over moderate heat, stirring, until the onions are softened, about 5 minutes. Uncover and cook the onions over high heat until golden brown, about 8 minutes longer. If the onions dry out, add a few tablespoons of water. Season the onions with salt and pepper, transfer to a plate and let cool slightly.
Punch down the dough and turn it out onto a lightly floured work surface. Divide the dough into 8 equal pieces. Roll each piece out to a 9-by-3-inch rectangle and arrange on the prepared baking sheets. Top the dough with the Fontina, sautéed onions and prosciutto. Bake for 25 minutes, or until golden and crisp.
In a large bowl, whisk the grapeseed oil, truffle oil and vinegar; season with salt and pepper. Add the apple and arugula and toss. Top the hot pizzas with the salad and serve immediately.