Preheat oven to 375F.
Place a large pot of water over high heat to boil the pasta. When the water reaches a bubble, salt it well, drop the shells in and cook them to al dente according to package directions. Drain the cooked shells and shock them under cold water to stop them from cooking. Reserve.
While the shells are cooking, mash up the tomatoes in the bottom of a casserole dish. Stir in the butter, basil, some salt and pepper into the dish, and set aside.
Place a large skillet over medium-high heat with 2 turns of the pan of EVOO, about 2 tablespoons. Add the garlic to the pan and cook until aromatic and light golden brown, about 1 minute. Add the spinach, and nutmeg to the pan, and cook to heat through.
Transfer the spinach to a large bowl and stir in the artichokes, ricotta, Parmigiano Reggiano, lemon zest, thyme, egg yolk, parsley, some salt and pepper. Fill the reserved pasta shells with the mixture, arranging them on top of the sauce in the casserole dish as you complete them.
Cover the casserole with aluminum foil and transfer to the oven. Bake covered for 20 minutes, then remove the foil and turn the oven up to 425F. Continue cooking until the filling is golden brown and bubbly, about 15 minutes more.
Serve 4 shells to each person topped with some of the sauce.