Melt the unsalted butter with olive oil in a large deep cast iron skillet or Dutch oven over medium heat. Add the thinly sliced yellow onions and 1/2 teaspoon of salt. Toss to coat the onions evenly in the fat.

Cook the onions for 20 to 25 minutes, stirring every 3 to 4 minutes, until they turn deeply golden brown, jammy, and sweet. If the bottom begins to brown too quickly, turn the heat down slightly and add a splash of water to lift the fond.

Stir in the minced garlic, fresh thyme leaves, Worcestershire sauce, and apple cider vinegar. Cook for 1 to 2 minutes while scraping up all the savory browned bits from the bottom of the pan until fragrant.

Pour in the uncooked pasta shells and 3 1/2 cups of beef bone broth. Stir well and bring the liquid to a lively boil over medium-high heat.

Once boiling, reduce the heat to medium-low, cover with a tight-fitting lid, and let simmer for 10 to 12 minutes, stirring once halfway through, until the pasta is al dente and most of the broth is absorbed into a silky pan sauce.

Remove from heat. Stir in the heavy cream and half of the shredded Gruyère and grated Parmesan until melted and glossy. Scatter the remaining Gruyère across the top. Cover for 2 minutes (or pop under the oven broiler for 2 minutes) until the cheese turns bubbling and golden. Garnish with fresh chives and thyme, then serve warm.