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1
Cut tops from tomatoes about 3/4 in. from stems (keep leaves and small stems attached) and set aside. Working over a food processor and using a teaspoon, carefully scoop out tomato pulp and juices, leaving only the outer walls. Puree pulp and juices, then measure; you should have 2 cups. Trim a very thin slice from base of tomatoes so they sit flat (if you get a hole, patch from the inside with a tomato slice).
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2
Heat 3 tbsp. oil in a medium saucepan over medium heat. Cook onion and garlic, stirring occasionally, until lightly browned, about 5 minutes. Add rice, kosher salt, pepper, and chile flakes, stirring to coat. Stir in tomato puree and 1/4 cup water.
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3
Cook uncovered, stirring occasionally, until liquid is reduced to the surface of rice, 8 to 10 minutes. Reduce heat to medium-low, cover, and cook, stirring once or twice, until rice is cooked through, about 15 minutes.
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4
Meanwhile, preheat oven to 450u00b0 with a rack in the top third of oven. Grease a shallow baking dish with some of remaining oil. Stir parsley, basil, and cheese into risotto. Divide risotto evenly among tomato shells, mounding it a bit, and set in oiled dish, rice side up. Brush reserved tomato tops with oil and loosely set on tomatoes. Sprinkle tops with sea salt if you like.
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5
Bake until tomatoes soften a bit, 12 to 15 minutes. Serve warm or at room temperature.