Melt 2 tablespoons butter in a large skillet over medium-high heat. Cook and stir onions, thyme, and bay leaf in the butter for 5 minutes; season with salt and pepper. Reduce the heat to medium-low and cook until onions are browned, 10 to 15 minutes. Transfer to a plate and discard the bay leaf. Reserve the skillet.
Bring a large pot of lightly salted water to a boil. Cook elbow macaroni in the boiling water, stirring occasionally, until tender yet firm to the bite, about 8 minutes.
Meanwhile, melt remaining butter in the reserved skillet over medium heat. Whisk in flour for 1 minute, then whisk in beef broth and milk and bring to a boil; season with nutmeg, salt, and pepper. Reduce heat and cook until thickened, about 5 minutes. Stir in Gruyere cheese until melted.
Drain macaroni and toss with onion and sauce until well combined.
You can use penne rigate instead of elbow macaroni.
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