Preheat the oven to 450° F. In a skillet, combine the olive oil, shallots, and thyme, cook over medium heat until the oil is hot. Reduce the heat to low, cover, and cook 10-20 minutes, until the shallots are very soft and caramelized. Stir and cook another 5 minutes. Add the chili flakes. Remove from the heat.On a lightly floured surface, push the dough out until it's thin (about a 10-12 inch circle). Transfer the dough to a baking sheet. Mix the grated tomato with the garlic, salt, and pepper. Spread the fig preserves and tomatoes over the dough. Add the goat cheese, bacon, and basil. Top with mozzarella. Pull the shallots apart and arrange them over the cheese. Bake for 10-15 minutes or until the crust is golden and the cheese is bubbling. Remove from the oven and top with fresh basil. Slice and enjoy!