Bring a medium saucepan of water to a boil. Using a vegetable peeler, peel 1-inch-wide strips of zest from the lemon. In a large Dutch oven or skillet, heat the olive oil, onions, lemon peel and red-pepper flakes over medium. Season with salt and pepper, and cover. When you hear sizzling, uncover, reduce heat, and gently simmer, stirring occasionally, until the onions are very soft and golden at the edges, 20 to 25 minutes. If at any point the onions risk burning, reduce heat and add 1 or 2 teaspoons of water. Remove from heat.

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