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Heat oil in a 12-inch heavy skillet over medium heat until it shimmers. Add pine nuts and toast, stirring, until golden, about 2 minutes. Transfer to a plate with a slotted spoon.
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Add garlic to oil remaining in skillet and cook, stirring, until golden. Add onions and 1/4 tsp salt and cook, stirring occasionally, until softened, about 8 minutes. Add vinegar and cook, stirring, until most is evaporated, about 2 minutes. Add beet stems, 3/4 cup water, and 1/2 tsp salt and cook, covered, stirring occasionally, until stems begin to soften, about 12 minutes.
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Cook penne in a pasta pot of boiling salted water (2 Tbsp salt for 6 qt water) until al dente. Reserve 1 cup pasta-cooking water, then drain pasta.
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Meanwhile, add raisins, then beet leaves to onion mixture in handfuls, turning each handful with tongs until beet leaves are wilted before adding next batch. Add remaining 1/4 cup water and 1/4 tsp salt and cook, covered, stirring occasionally, until just tender, 5 to 6 minutes. Add olives, then add pasta and cook, tossing and moistening with some of the cooking water as necessary, just until liquid has thickened slightly. Serve sprinkled with pine nuts.
