Place a saucepan of water over a high heat, bring to the boil and stir in the macaroni pasta, and cook for ten minutes. Then drain and set aside. Keep back a few tablespoons of the pasta cooking water, which you can stir into the macaroni, to keep it from clumping together.
While the pasta is cooking roast the butternut squash. Toss the squash in one tablespoon of olive oil, season with sea salt and freshly ground black pepper. Roast in the oven for 20 minutes.
Next make the cheese sauce by melting the butter in a saucepan over a low heat, and then stir in the flour. Keep stirring for a couple of minutes until the flour is cooked and it looks like a lump of pastry dough. Then whisk in the milk, and continue to whisk until you get a thick and creamy sauce. Stir in the grated fresh nutmeg and Dijon mustard. Grate in the cheese and season with sea salt and freshly ground black pepper.
Stir the cheese sauce and the roasted butternut squash into the pasta, making sure all the pasta is coated in the cheese sauce. Then pour into a baking dish.
For the topping place a frying pan over a medium heat and melt the butter and stir in the breadcrumbs, chopped pecans and fresh thyme. Toast in the frying pan for two to three minutes. Then sprinkle over the top of the pasta and cheese sauce in the baking dish.