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Combine the cottage cheese, ricotta cheese, 1/2 cup mozzarella and parsley in a bowl and stir with a fork to incorporate and set aside. Cook pasta until tender but still firm, a minute or 2 less than the package directs. Drain.
Heat the oil in the same pot over medium heat. Add the onion and cook stirring occasionally, until translucent, about 5 minutes. Add the garlic and cook for 30 seconds more. Add the tomatoes, tomato sauce, oregano, rosemary, chili flakes, salt and pepper. Bring to a boil, then reduce heat and simmer for 10 minutes until sauce thickens slightly. Return pasta to pot with sauce and turn off heat. Add cottage cheese mixture.
Spray a 9 by 13-inch glass baking dish with cooking spray then transfer pasta mixture to pan. Top with remaining 3/4 cup mozzarella and the parmesan. Bake until heated through and cheese is melted, 30 minutes.