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For the Sauce
Warm the oil a large saucepan over medium heat. Add in the onion and cook until softened, about 6 to 8 minutes.
Add in the garlic and crushed chili flakes and cook for another minute, or until fragrant.
Stir in the wine, if using, and cook for 2 minutes. Then add in the crushed tomatoes, salt, and pepper, stir well to combine.
Bring sauce to a boil, then reduce to medium-low and simmer, stirring occasionally, for 45 minutes.
Stir in the sugar and basil and cook for another 15 minutes. Taste and add salt and pepper as needed.
Remove from heat allow to slightly cool before using it in the baked ziti. Sauce can be made up to 3 days in advance and stored in the fridge until needed.
For the Cheese Filling
In a large bowl, combine the ricotta cheese, parmesan cheese, mozzarella cheese, parsley, basil, egg, eggs, salt and pepper. Stir together until just smooth. Set aside until needed.
For the Shells
Bring a large pot of water to boil. Add a 1/2 teaspoon of salt, then stir in the pasta shells. Set a timer and cook for exactly 4 minutes. Drain and quickly run under cold water to stop the cooking process. Pat the shells dry and set aside.
Assembly and Baking
Preheat the oven to 375 degrees (F).
Pour 1 and 1/2 cups of the tomato sauce onto the bottom of a 9X13-inch casserole dish. Set aside.
Stuff each shell with a heaping tablespoon of the cheese filling, then place it in the baking dish. Nestle the shells as close together as possible. Repeat with all shells until you run out of cheese filling.
Top shells with remaining pasta sauce, then sprinkle with both cheeses.
Bake the shells for 35 minutes, or until the cheese is golden and bubbling.
Let rest for 5 minutes before serving. Then sprinkle with parsley and parmesan and serve!
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