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In a medium skillet, melt 1 tablespoon butter over medium-high heat. Add bread crumbs and cook, stirring until butter is absorbed and bread crumbs are toasted. Remove from heat and set aside.
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Bring a large pot of water to a boil over high heat. Prepare and ice-water bath; set aside. Season boiling water generously with salt and return to a boil. Add broccoli rabe and cook until crisp-tender, about 2 minutes. Drain and transfer to water bath to cool. Cut crosswise into 1-inch pieces, separating leaves and florets from stems.
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In the bowl of a food processor, combine broccoli rabe stems, 1/4 cup olive oil, Parmesan, pine nuts, lemon peel, and a pinch of salt. Pulse just until a smooth pesto is formed; set aside.
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Bring another large pot of water to a boil over high heat. Generously salt water and return to a boil. Add pasta and cook until al dente, about 7 minutes; drain, reserving 1/4 cup pasta cooking water.
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Meanwhile, in a large skillet over medium-high heat, heat remaining tablespoon oil until hot. Add garlic, red-pepper flakes, and a pinch of salt; cook until garlic is soft and translucent, about 1 minute.
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Add broccoli rabe florets and leaves to skillet along with reserved pasta cooking water; cook, stirring, until broccoli rabe is warmed through. Add pasta and pesto to skillet; season with pepper and butter. Toss to combine. Serve immediately with toasted bread crumbs and Parmesan.