Cook the chopped onion in melted butter and oil 1 to 2 minutes, then add flour and cook together 1 to 2 more minutes. Stir in stock, then combine with cooked butternut squash until heated. Stir in cream or half-and-half and bring sauce to a bubble. Stir in cheeses and season the completed sauce with salt, nutmeg and pepper. Taste to adjust seasonings.
Drain cooked pasta well and combine with sauce. Put in a baking dish and top with breadcrumbs mixture and bake until golden at 350 for no more than 20 minutes.
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