In a large bowl toss the cubed bread with the olive oil. Pour this out onto a baking sheet and toast the bread for 12 minutes, flipping the bread halfway through until lightly golden brown. Set aside. Turn the oven off.
In a heavy bottom skillet (or dutch oven) with deep sides over medium-low heat, melt the butter.
Add the onions, garlic, thyme, salt, and pepper, stir to combine. Once the onions are coated in the butter, turn the heat down to low and cook for 2 hours to caramelize the onions, uncovered. Stir frequently to make sure they do not burn. Onions are done when they are cooked down to about a cup and are a very deep brown color.
While the onions are browning, cook the pasta per the directions on the back of the box and drain well.
Preheat the oven to 400°F. Spray a 9x13 baking dish with cooking spray, set aside.
When the onions are done cooking, discard the thyme sprigs, take out about ¼ cup of the onion mixture, and set aside. Add the flour to the pot and stir to combine in the fat, cook for 2 minutes. Slowly pour in the half & half, whisking constantly.
Bring to a simmer to thicken and take off the heat. Stir in 1 cup of the Gruyere and the 3 cups of white cheddar cheese until melted. Mix the cheese sauce with the macaroni noodles and pour into the baking dish, smooth out the top.
Evenly distribute the leftover onions on top of the casserole. Top the casserole with the croutons. Add the remaining 3 cups of the Gruyere on top.
Bake for 15-20 minutes until bubbly and the cheese is browned on top. Be careful not to burn the croutons. Garnish with optional parsley and serve.
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Notes
Baked mac and cheese will keep in the refrigerator for 3 to 4 days. Store covered or transfer to a separate container with a lid.For best results, reheat individual portions in a pan on the stove or pop the pan back in the oven until warmed through.