In a large pot (non-stick works great) or Dutch oven over medium-high heat, add the butter (¼ stick), the onions (4 large), and ½ tsp kosher salt.

Add the lid and cook for 10 minutes undisturbed to help sweat the onions.

Remove the lid, reduce heat to medium, and continue cooking, stirring occasionally until the onions have reduced significantly and start to turn light brown / stick to the bottom of the pot.

Reduce heat to medium-low and continue cooking and stirring frequently until the onions have turned a rich brown color, about 1.5 hours in total.

If onions are sticking too much, add a bit of hot water and use that to scrape them off the bottom. Remove onions to a small bowl.

Meanwhile, toward the end of cooking the onions, bring a large pot of water to a boil. Season with a large handful of kosher salt.

Boil the pasta (1 lb) until al dente. Drain (to keep pasta from sticking together, either drizzle with some oil or keep it sitting in a few cups of the pasta water).

Preheat oven to 400 °F.

In the pot you just used for pasta again, heat over medium and add remaining butter (¾ stick) and the flour (¾ cup). Cook, whisking constantly, for 2 minutes.

Gradually whisk in the milk (4 cups). Then add the cheeses (1 lb) (reserve about 20% for topping the mac) and half of the caramelized onions.

Season with salt to taste and A LOT of pepper. Then stir in the drained pasta. Taste for seasoning again.

Add to a large baking dish. Top with remaining cheese and dot with the remaining onion.

Cover with foil and bake for 30 minutes. Then remove foil and continue baking until golden brown, another 20 minutes.

Garnish with chives and serve hot.