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Preheat oven to 425 degrees F.
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Place squash on a foil lined baking sheet covered with cooking spray.
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Combine ¼ teaspoon salt, rosemary and pepper and sprinkle on the squash.
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Bake squash at 425 degrees F for 25-30 minutes or until tender and lightly browned. Remove from oven and increase temperature to 450 degrees F.
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While squash is roasting, cook bacon in a large nonstick skillet over medium heat until crisp. Remove bacon from pan, reserving 1 ½ teaspoons of the drippings in the pan. Crumble the bacon. Add shallots to the pan and sauté 8 minutes or until tender.
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Add the roasted squash to the bacon and shallots and stir to combine. Set aside.
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Cook pasta according to package directions. Drain well.
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Combine flour and ½ teaspoon salt in a Dutch oven over medium high heat. Gradually add the milk, stirring constantly with a whisk. Bring to a boil.
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Cook 1 minute or until slightly thick, stirring constantly. Remove from heat. Add provolone, stirring until cheese melts.
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Add pasta to cheese mixture, tossing well to combine.
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Spoon pasta mixture into an 11 x 7 inch baking dish lightly coated with cooking spray; top with squash mixture. Sprinkle evenly with Parmesan cheese. Bake at 450 degrees F for 10 minutes or until cheese melts and begins to brown.