In a large Dutch oven or heavy bottomed pot, melt the butter over medium heat. Add the sliced onions and a pinch of salt. Cook, stirring occasionally, for 25 to 30 minutes, until the onions are deeply golden and soft.

Once the onions are caramelized, add the minced garlic and fresh thyme. Cook for 1 minute until fragrant.

Sprinkle the flour over the onion mixture and stir constantly for about 2 minutes.

Slowly pour in the beef broth while stirring. Scrape up any browned bits from the bottom of the pot. Bring to a simmer and cook for 3 to 4 minutes, until slightly thickened. Then reduce the heat to low and stir in the heavy cream. Let it simmer gently for another 2 minutes. At this point, taste and season with salt and pepper.

While the sauce simmers, bring a large pot of salted water to a boil. Cook your pasta according to package directions until al dente. Reserve about 1 cup of pasta water before draining.

Add the drained pasta to the sauce and toss gently. If the sauce seems too thick, add a splash of reserved pasta water until it coats the pasta beautifully. Then stir in the shredded Gruyere and Parmesan. The cheese should melt into a silky, creamy blanket.

Spoon the pasta into bowls, garnish with fresh thyme leaves and an extra sprinkle of Parmesan. Serve hot.