In a large soup pot or Dutch oven, heat the olive oil over medium heat. Add the pepper flakes and cook for 15 seconds. Add the onion and cook, stirring occasionally, until golden brown, about 15 minutes. Add the garlic and cook until fragrant, about 1 minute. Stir in the tomato paste and cook, stirring constantly, for 1 minute. Add the tomatoes one at a time, crushing them by hand as you go. Season with 1 teaspoon salt and pepper to taste. Simmer the sauce over low heat, covered. Heat a large skillet over medium-high heat. Add the beef, pork, veal, savory, thyme, oregano, and fennel seeds. Season with 1 teaspoon salt and pepper. Break up the meat with a wooden spoon, and cook until it loses its raw color, about 7 minutes. Add the meat to the sauce, holding back any excess fat. Add the rind of the Parmesan, if using. Simmer the sauce, covered, over low heat, for 1 1/2 hours. (If the sauce gets too thick adjust the consistency with water.) Taste and season with salt and pepper to taste. Just before serving, remove the Parmesan rind and add the grated cheese. Cook's Note: 3 to 4 cups of this sauce will dress 1 pound of pasta, like spaghetti or rigatoni. It is also perfect for lasagna. This sauce freezes very well.
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