1Sauté the finely chopped onion for a few minutes with salt and pepper.
2Add the minced garlic and cook for 30 seconds, then add the chopped spinach.
3Season again with salt and squeeze in the juice from half a lemon.
4Let the spinach wilt and then set aside, making sure to squeeze out as much water as possible.
5To make the marinara, heat about 1/4 cup of olive oil in a clean pan over medium/low heat.
6Add the sliced garlic, basil leaves, and Calabrian chilies, and let them sizzle for a couple of minutes.
7Pour in the crushed tomatoes, season with salt and pepper, and let it simmer.
8Cook the pasta shells to al dente, drain, and set aside.
9Combine ricotta, mozzarella, Parmesan, cooked spinach, fresh basil, fresh parsley, salt, pepper, red pepper flakes, lemon zest, nutmeg, and an egg in a bowl.
10Stir to combine the filling ingredients and set aside.
11Add a thin layer of marinara sauce to the bottom of a baking dish.
12Stuff each pasta shell with about 2 to 3 tablespoons of the ricotta filling.
13Arrange the stuffed shells in the baking dish and dollop in any leftover ricotta filling.
14Pour the tomato sauce directly on top of the shells.
15Finish with a layer of mozzarella and Parmesan cheese.
16Cover the dish with foil and bake at 350°F for 20 minutes.
17Remove the foil and finish under the broiler until golden and bubbly.