Unwrap the ricotta cheese from the cheesecloth; the texture should be pretty dry and crumbly. If it is really dry (this is good) pass it through the food mill with the biggest holes. Put the cheese into a large bowl.
Finely chop the squeezed spinach and add it to the ricotta. Add the eggs, grated Parmigiano-Reggiano and nutmeg. Mix until well combined. Taste and season with salt, if needed. Add in 1/4 cup of flour. If the mixture is still very wet, add in the remaining 1/4 cup of flour.
Dust a sheet tray generously with flour. Coat another sheet tray generously with semolina flour. Fill a pastry bag with the ricotta/spinach mixture. Pipe 1 1/2-inch balls of the cheese mixture onto the all-purpose flour lined tray. Shake the tray around to coat the balls in flour. Roll each flour coated cheese piece around in your hand to form a ball. Do this gently so as to not squish the cheese balls. Arrange them on the semolina lined tray.
Bring a saucepan full of water to a boil over medium heat. Set up a bowl of ice water. In the bottom of each tomato cut an "X" in the skin. Working in batches, put the tomatoes in the boiling water for 15 to 20 seconds ONLY! Remove the tomatoes from the boiling water and put them immediately into the ice water. When the tomatoes have cooled, remove them from the ice water and the skin should come off very easily.
Remove the stems and seeds from the tomatoes; coarsely chop the tomatoes and reserve.
Coat a large straight-sided saute pan, over medium-high heat, with olive oil. Add the onions, season with salt, to taste. Toss in the crushed red pepper and cook the onions until they are soft and aromatic, about 8 to 10 minutes. Add in the garlic and cook for 2 to 3 more minutes. Stir in the tomatoes and season with salt, to taste. Bring the tomato mixture to a boil, then reduce the heat and simmer for 15 to 20 minutes. Taste and adjust the seasoning, if needed.
Toss in the basil just before serving.
Bring a large pot of well-salted water to a boil over medium heat, then reduce the heat until the water is at a simmer. Carefully add the gnocchi to the simmering water. Cook until the gnocchi float and have begun to swell, 3 to 5 minutes.
On individual serving plates, spoon some sauce on each plate and spread it out until it becomes a 4 to 5-inch circle.
Using a spider or long handled mesh strainer, carefully remove the gnocchi from the cooking water, blot on a tea towel and arrange 5 gnocchi on each circle of sauce. Sprinkle with Parmigiano-Reggiano and serve.