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Chile-Braised Short Ribs

['2 1/2 lb. (2"-thick) cross-cut bone-in short ribs (flanken style), cut into 2x2" pieces', 'Kosher salt', '2 dried guajillo or ancho chiles, seeds removed', '1 large onion, sliced into 1/2"-thick rounds', '5 garlic cloves, unpeeled', '1 tsp. crushed red pepper flakes', '1 tsp. ground coriander', '1 tsp. ground cumin', '1/2 tsp. ground cinnamon', '3 Tbsp. vegetable oil, divided', '2 Tbsp. tomato paste', '1/2 acorn squash (about 1 lb.), seeds removed, sliced lengthwise into 1"-thick wedges', 'Plain whole-milk Greek yogurt', 'cilantro sprigs', 'and lime wedges (for serving)']

Season ribs with salt. Let sit at room temperature 1 hour, or chill, uncovered, up to 12 hours. If chilling, let sit at room temperature 1 hour before cooking.
Meanwhile, place chiles and 5 cups hot water in a blender and let sit while you prep onion and garlic.
Heat broiler. Broil onion and garlic on a rimmed baking sheet, undisturbed, until charred on top (don’t worry if they get super dark), 8–10 minutes.
Pop garlic out of their skins and place garlic, onion, red pepper flakes, coriander, cumin, and cinnamon in blender with chiles. Blend until smooth but still speckled with chiles; season purée lightly with salt. Set aside.
Heat 2 Tbsp. oil in a medium heavy pot over medium-high. Working in 2 batches, cook ribs, turning occasionally and reducing heat if needed, until browned all over, 10–12 minutes per batch. Transfer to a plate.
Carefully pour off oil and wipe out pot. Pour remaining 1 Tbsp. oil into pot and place back over medium-high heat. Add tomato paste and cook, stirring often, until tomato paste begins to separate and stick to pot, about 3 minutes. Stir in chile purée. Return ribs to pot and bring liquid to a simmer. Partially cover pot and cook, reducing heat to low to maintain a very gentle simmer, turning ribs occasionally, and skimming any excess fat from surface, until meat is very tender, 3–3 1/2 hours. (If sauce gets thick before meat is done, add water as needed to thin out a bit.)
Add squash to pot and push down so it’s mostly submerged. Bring to a simmer and cook, uncovered, until squash is tender and liquid is thickened and saucy, 18–20 minutes.
Serve ribs and squash, topped with yogurt and cilantro, with lime wedges.
Do Ahead: Ribs (without toppings) can be made 3 days ahead. Cover and chill.

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