Step 1: Caramelize the Onions

1. Heat 4 tsp of olive oil in a skillet over medium heat. Once it glistens, add the thinly sliced onions.
2. Cook the onions for 8-10 minutes, stirring often until they turn translucent. Add 1/2 tsp of kosher salt, then reduce the heat to medium-low.
3. Continue to cook, stirring every 5-10 minutes, until the onions reach your desired level of caramelization. Deeply caramelized onions can take an additional 40-50 minutes.
4. Once the onions are caramelized, add 2 tbsp of dry white wine to deglaze the pan. Remove the onions from the pan and reserve them to the side.

Step 2: Preheat the Oven and Prepare the Breadcrumb Topping

1. Preheat your oven to 425° Fahrenheit (220° Celcius).
2. Grease a 2.5 qt baking dish with 1 tsp of butter and reserve it to the side.
3. In a small bowl, stir together the panko breadcrumbs, 1/4 tsp of dried thyme, and 1 tsp of melted butter. Reserve this breadcrumb mixture to the side.

Step 3: Cook the Pasta

1. Cook your chosen pasta according to the package instructions, reducing the cooking time by 1 minute.
2. Drain the pasta and toss it with 1 tsp of butter. Reserve it to the side.

Step 4: Create the Cheese Sauce

1. In a large pot over medium heat, melt 6 tbsp of unsalted butter.
2. Once melted, add the all-purpose flour. Whisk constantly for 1-2 minutes until the mixture is emulsified and bubbly.
3. While whisking, slowly pour in the whole milk until the mixture is well combined.
4. Add the beef bouillon paste and Dijon mustard, then season with 1/2 tsp of dried thyme, a pinch of ground nutmeg, 1/2 tsp of kosher salt, and 1/4 tsp of cracked black pepper.
5. Continue whisking until the sauce is thick and smooth.
6. Add the shredded Gruyere cheese and mozzarella cheese in 2 batches, whisking after each addition until the cheese is melted and the sauce is smooth. Taste for salt and pepper and adjust if needed.

Step 5: Assemble and Bake

1. Add the reserved pasta to the pot and gently fold it in until it's well-coated and saucy.
2. Transfer the mixture to the prepared baking dish.
3. Top the mac & cheese with the reserved caramelized onions and the seasoned breadcrumb mixture.
4. Bake for 15-20 minutes or until the breadcrumbs turn golden brown, and everything is warm and melty.