This elevated take on a traditional Thanksgiving side combines the sweetness of caramelized onions with the creamy tang of two kinds of cheese. The crunchy French fried onion topping -- everyone's favorite Thanksgiving garnish -- adds the perfect counterpoint to all that creaminess.
Bring a large pot of salted water to a boil over high heat. Add the pasta and cook until just slightly softened, about 6 minutes. Reserve 1 cup pasta cooking water, then drain the pasta and rinse under cold water.
Melt 3 tablespoons of the butter in a large skillet over medium heat. Add the onions, sprinkle with the thyme, sugar and 1/2 teaspoon pepper and cook, stirring occasionally, until dark brown, about 20 minutes. Add the wine and bouillon cube and stir to dissolve the bouillon. Cook until the liquid is reduced by half, about 5 minutes. Set aside.
Melt 4 tablespoons butter in a large heavy-bottomed saucepan or Dutch oven over medium heat. Whisk in the flour, mustard powder and cayenne. Cook, whisking constantly, until smooth and slightly golden, about 2 minutes. Whisk in the milk. Cook, whisking occasionally, until the sauce begins to boil and thicken, about 7 minutes; remove from the heat. Stir in the Cheddar and 2 cups of the Gruyere until fully melted. Stir in the pasta, adding the reserved pasta water as needed to make a creamy sauce. Season with salt and pepper.
Melt the remaining 1 tablespoon butter in a small bowl in the microwave. Brush a 9-by-13-inch metal baking dish with the melted butter. Spread half the pasta mixture in the prepared dish. Top with the onion mixture in an even layer, then cover with the remaining pasta mixture. Sprinkle with the remaining Gruyere.
Bake until heated through and just bubbling, about 20 minutes. Top with the French fried onions and return to the oven for 5 minutes. Let rest for 10 minutes, then sprinkle with the chives before serving.
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