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Bring a large pot of water to a boil. Season generously with salt. Add rigatoni and cook until al dente according to package directions. Drain; return to pot and cover.
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Heat a large skillet over medium-high heat. Add sausage. Cook until well browned on both sides, about 5 minutes. Remove sausage to a bowl;set aside.
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Reduce heat to medium. Add butter to the same skillet. Once butter is melted, add flour and whisk to combine. Cook for 1 minute. Slowly pour in milk while whisking to prevent any lumps from forming. Bring sauce to a simmer, whisking often. Once bubbling, add cheese. Stir until cheese is melted. Season with salt and pepper to taste.
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Pour sauce over cooked pasta, add kielbasa and half the apples. Stir to combine. Portion pasta, and top with remaining apples - distributing evenly among the dishes. Serve immediately.