While pasta cooks, heat a large heavy bottomed pot over medium heat. Add EVOO and butter. When butter melts into oil add thyme and grate onion directly into the pot. Cook the grated onions for 1-2 minutes, then add flour and cook together for 1-2 minutes. Whisk in the stock, then add the squash and cook until warmed through and smooth. Stir in the cream and bring sauce to a bubble. Stir in the cheeses and season with salt, nutmeg and pepper to taste.
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