French Onion Baked Mac and Cheese

Name: French Onion Baked Mac and Cheese
Ingredients: Kosher salt and freshly ground black pepper; 1 pound elbow macaroni; 1 stick (8 tablespoons) unsalted butter; 4 onions, thinly sliced; 2 teaspoons fresh thyme leaves; 1 teaspoon granulated sugar; 1 cup white wine; 1 beef bouillon cube; 1/4 cup all-purpose flour; 2 teaspoons mustard powder; 1/4 teaspoon cayenne; 3 cups milk; 1 pound sharp yellow Cheddar, grated (about 4 cups); 1 pound Gruyere, grated (about 4 cups); One 6-ounce container French fried onions; Chopped chives, for topping