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Preheat oven to 400F.
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Place macaroni in a large heat proof bowl, pour boiling water over top with a pinch of salt. After 5 minutes stir the pasta to ensure that it does not stick together. Let sit for 30 minutes.
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As the pasta soaks, in a saucepan, melt butter over medium heat. Once melted, whisk in the flour and cook until golden making a roux, about 1 minute.
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Slowly add the milk stirring constantly, heat until thickened and bubbling at the edges, about 4 minutes.
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Remove from the heat and stir in the cheddar, cayenne, nutmeg, salt and pepper. Set aside.
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Once pasta is done soaking, drain and mix with the cheese mixture until well coated.
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Transfer to a casserole dish and bake for 25 minutes covered, then uncovered until golden under the broiler, about 5 minutes.