In a large skillet, heat butter over medium until melted. Add the onions and stir to coat. Let the onions sweat, stirring frequently, for about 10 minutes, or until they begin to soften, but remain white and translucent.

Reduce heat to medium-low and continue to cook the onions, over the next 50 minutes. In a small bowl, stir the boullion paste into 1/2 cup of very hot water until it's fully dissolved and keep near the stove. The onions will reduce as they release more moisture and begin to take on golden hues. Keep an eye on everything, stirring often, and don't let the onions dry out and begin to brown on their edges. If they do, reduce the heat further and add a teaspoon or two of the boullion liquid to the pan, mixing well with the onions to keep them moist.

When the onions are golden, very reduced, and seem almost melty, they're finished. Reduce heat to low to hold until ready to use.

Preheat the oven to 375ºF, and rub the interior of a 13x9" baking pan with butter or oil to minimize sticking.

Cook the elbow macaroni in a large 3-quart pot according to the directions on the box. While the pasta cooks, make the cheese sauce.

In a medium pot, heat 3 tablespoons of butter over medium until melted. Stir the flour and let heat for a minute to cook off the rawness of the flour. Stir in the dairy one cup at a time, whisking to create a smooth, lump-free texture. Increase heat to medium high and let the sauce base bubble and thicken. When the sauce clings easily to the back of a spoon, stir in 3 cups of the shredded cheese (reserving 1 cup for the topping), a handful at a time, incorporating it completely before the next handful. When the cheese sauce is smooth, stir in the Worcestershire sauce and a big pinch of black pepper.

When the pasta finishes cooking, drain completely and return to the pot.

Fold the caramelized onions into the pasta, followed by the cheese sauce.

Pour the pasta into the prepared baking pan and even out the top. The onions may or may not be visible — that's okay. They're there for flavor, not for bling!

Melt one tablespoon of the butter in the skillet that cooked the onions. Pour the Panko bread crumbs over the melted butter and stir until golden (just a couple of minutes).

Cut the remaining tablespoon of butter into small cubes and position around the mac and cheese, and distribute the cup of shredded cheese.

Sprinkle the breadcrumbs evenly over the mac and cheese.

Bake for 25 to 30 minutes, or until the mac and cheese is bubbly or sizzling. Remove from the oven and let rest for a few minutes before serving. Sprinkle fresh thyme leaves over the topping.