Bring a large pot of water to a boil, salt it, add the pasta and cook according to package directions until al dente; drain.
While the pasta is working, heat a large, deep skillet over medium-high heat. Add the butter to melt, then add the onions, bay leaf and thyme; season with salt and pepper. Cook, stirring occasionally, until the onions are light caramel in color, 15 to 20 minutes.
Preheat the broiler. Discard the bay leaf. Stir the flour into the onion mixture. Stir in the milk and beef stock and bring to a boil. Cook, stirring, until thickened, about 2 minutes. Remove from the heat and stir in 1 1/2 cups cheese until melted, then stir in the mustard.
Add the pasta to the sauce and toss. Spoon into a 9-by-13-inch casserole dish, top with the remaining 1 cup cheese and broil until brown, 2 to 4 minutes. Top with the chives and serve immediately.