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Step 1
Preheat oven to 325°F.
Step 2
In an 8-by-12-inch casserole dish, toss together tomatoes, garlic, shallots,1 teaspoon salt and pepper to taste. Pour the olive oil over everything, then toss to combine. Top with thyme sprigs.
Step 3
Bake until the vegetables are soft, about 45 minutes, stirring once during cooking.
Step 4
While the tomatoes are cooking, bring a large pot of salted water to a boil. Cook pasta until al dente, or according to package instructions. Drain and place cooked pasta in a large bowl and add a few cups of tomato and shallot confit with the juices, tossing to combine. Taste and adjust seasoning with a little more salt and pepper, to taste.
Step 5
Place the remaining tomato confit in a separate bowl.
Step 6
To serve, stir in the basil, a sprinkle of red pepper flakes (if using) and serve right away, passing additional tomato and shallot confit* and pecorino, or Parmigiano-Reggiano, at the table.