In a large skillet, melt 2 tablespoons of butter over medium heat. Add the sliced large yellow onions and a pinch of kosher salt. Stir frequently for about 20-30 minutes until the onions turn a deep golden brown and become soft and caramelized.

While the onions are caramelizing, bring a large pot of salted water to a boil. Add the cavatappi pasta and cook according to the package instructions until al dente, around 7-9 minutes. Drain the pasta and set aside.

In a medium saucepan, melt the remaining 4 tablespoons of butter over medium heat. Whisk in the all-purpose flour for about 1 minute. Gradually add the whole milk while whisking until smooth and slightly thickened, about 3-5 minutes. Mix in the grated fontina, Gruyère, and shredded sharp white cheddar until fully melted and creamy.

Once the cheese sauce is ready, stir in the caramelized onions and cooked cavatappi pasta until well coated.

Preheat your oven to 350°F (175°C). Transfer the macaroni mixture to a greased baking dish or individual ramekins. Bake for 25-30 minutes or until the top is golden brown and the edges are bubbling.

Let it sit for a few minutes, then sprinkle fresh thyme leaves on top and serve warm.