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Preheat oven to 350 degrees F.
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Add olive oil to a medium/large skillet. Heat for thirty seconds over medium/low heat. Add onion to the pan and saute for four minutes, until translucent. Add garlic and mix to combine, saute one more minute.
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Turn heat to low, add in the kale. Cover with a lid and cook for about five minutes. Remove lid and stir kale to combine with onion and garlic. Add in ½ the lemon zest and the lemon juice. Season with salt, pepper, nutmeg, and crushed red pepper flakes if you are using them. Stir to combine and cover with lid. Cook for another ten minutes, until all the kale is wilted.
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Remove lid, add in the cream cheese. Wait a few minutes for the cream cheese to start to melt. As the cream cheese melts, mix to evenly coat all of the kale.
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Once all the cream cheese has melted, mix in ½ cup of grated parmesan. Turn off the heat. Transfer kale to a small baking dish (6 inch round or a 3 cup rectangular Pyrex dish). Top with remaining parmesan and lemon zest. Drizzle lightly with olive oil. Bake for 10-15 minutes until golden.
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Let the dish cool for about seven minutes before serving.