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In a medium-sized skillet, melt the butter on low heat.
Chop the onions into thin two-inch slices and cook with butter until caramelized.
Preheat the oven to 350F (175C) and grease a casserole dish.
Mix spätzle noodles, caramelized onions, sour cream, Emmentaler cheese, eggs, cottage cheese, nutmeg, salt, and pepper in a bowl.
Pour the mixture into the casserole dish, sprinkle with reserved cheese, and bake for 40 minutes.
Cut into pieces and serve hot.