Combine the tomatoes and olive oil in a large skillet over medium high heat.
As the oil starts to get hot, and the tomatoes start to blister, reduce the heat to medium and let simmer for 20 minutes, stirring occasionally. The last 5 minutes, add the garlic, salt, pepper and red pepper flakes and stir to combine
Once the tomatoes start to fall apart, remove them from the heat and let cool in the skillet for about 20 minutes, stir in the basil to wilt.
Cook the pasta until al dente while the tomatoes are cooling. Reserve about 1/2 cup of the pasta water once cooked and add to the tomato confit if needed to loosen it up, stir everything into the pasta. Adjust seasoning as needed and serve with fresh basil and chives.