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Winter Squash and Short-Rib Enchiladas

['1 teaspoon coriander seeds', '2 tablespoons cumin seeds', '7 guajillo chiles, seeds removed', '2 ancho chiles, seeds removed', '5 morita chiles', '4 1/2 cups homemade chicken stock or low-sodium chicken broth, divided', '8 cloves garlic, peeled', '2 tablespoons tomato paste', '1 teaspoon crushed Mexican or Italian oregano', '1 medium red kuri squash or sugar pumpkin, halved, seeds removed', '1 tablespoon vegetable oil', '3 pounds English-style bone-in beef short ribs', 'Kosher salt', '2 bay leaves', '1 cup vegetable oil', '8 (6-inch) white corn tortillas', '8 ounces Oaxaca cheese or salted fresh mozzarella, grated', '1/2 cup unsalted, roasted pumpkin seeds (pepitas), coarsely chopped', '1/3 cup coarsely chopped marjoram or oregano', '2 tablespoons coarsely chopped mint', 'Kosher salt', '1/2 onion, thinly sliced', 'Lime wedges (for serving)', 'A spice mill or a mortar and pestle']

Toast coriander seeds in a small skillet over medium heat, swirling pan often and adding cumin seeds during the last 30 seconds of cooking, until fragrant, about 2 minutes. Let cool, then finely grind in spice mill or with mortar and pestle.
Bring guajillo, ancho, and morita chiles and 4 cups stock to a boil in a medium saucepan over medium-high heat. Cover, remove from heat, and let sit 30 minutes to let chiles soften.
Transfer chile mixture to a blender and add toasted spices, garlic, tomato paste, and oregano and purée until smooth, about 2 minutes.
Preheat oven to 250°F. Place squash, cut side down, in a 13x9" baking dish and bake until very tender, 2–2 1/2 hours. Let cool slightly, then remove skin and discard.
Meanwhile, heat oil in a medium heavy pot over medium-high. Season beef with salt and cook, turning occasionally, until browned on all sides, 10–12 minutes. Pour off excess oil and carefully add chile purée (it may bubble vigorously) and bay leaves. Bring to a boil, cover, and transfer to oven, next to squash. Braise beef until it shreds easily, 2–2 1/2 hours; season with salt.
Skim excess fat from chile sauce and transfer meat, leaving bones behind, to a baking sheet. Remove bones and bay leaves from sauce. Let beef cool slightly, then shred with 2 forks, discarding any cartilage or silver skin.
Blend sauce, 2 cups roasted squash, and remaining 1/2 cup stock in a blender until smooth, about 30 seconds; season with salt. Mix 1/2 cup squash-chile sauce into shredded beef and season with salt. Set remaining sauce aside.
Preheat oven to 425°F. Heat oil in a medium skillet over medium-high until it bubbles immediately when edge of tortilla touches the surface. Working one at a time, fry tortillas until just starting to brown and crisp, about 10 seconds per side (they should still be somewhat pliable). Transfer to paper towels to drain.
Dip both sides of each tortilla in squash-chile sauce just to coat and transfer to a rimmed baking sheet. Spread 1 cup sauce down the length of a 13x9" baking dish. Spoon 1/4 cup beef mixture across the center of a tortilla. Fold one side over filling, then continue to roll up tortilla. Place seam side down in prepared baking dish. Repeat with more sauce and remaining tortillas (enchiladas should be nestled right up against each other in pan). Top with cheese and remaining sauce. Bake enchiladas until sauce is bubbling and cheese is beginning to brown, 15–20 minutes. Let sit 10 minutes.
Meanwhile, toss pumpkin seeds, marjoram, and mint in a small bowl; season with salt.
Top enchiladas with onion and pumpkin seed mixture. Serve with lime wedges for squeezing over.
Short ribs can be braised and squash can be roasted 3 days ahead. Let meat cool in chile sauce (do not shred); cover and chill ribs and squash separately.

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