Preheat the oven to 425° F.
In a large baking dish, combine the tomatoes, onion, garlic, thyme, butter, salt, pepper, and chili flakes. Bake 20-30 minutes or until the tomatoes begin to char and release their juices.
Using an immersion blender or food processor, puree the tomatoes until smooth. Add cream if needed and return the sauce to the baking dish.
Meanwhile, bring a large pot of salted water to a boil over high heat. Boil the pasta until al dente according to package directions.
In a medium bowl, combine the ricotta, provolone, and ½ cup pesto.
To assemble, spoon 1 tablespoon of the cheese mixture into each shell, placing the filled shell into the baking dish full of sauce. Spoon the remaining pesto over the shells and add the mozzarella.
Bake for 15 minutes until the cheese is melted. Serve with fresh basil. Enjoy!
