Shredded Beef Ragu Pasta

Brown the beef first, then keep the covered pot at a gentle braise until the meat pulls apart easily. Penne catches the thick tomato sauce and the small shreds of beef. Use the full batch for dinner, or keep some sauce separate to freeze for another pot of pasta.
Ingredients
2½ pounds boneless beef chuck roast, trimmed of large hard pieces of fat and cut into 4 roughly equal pieces
1½ teaspoons fine sea salt, divided
½ teaspoon black pepper
3 tablespoons olive oil, divided
1 medium onion, finely diced
1 cup finely diced carrots
1 cup finely diced celery
3 garlic cloves, minced
3 tablespoons tomato paste
1 cup dry red wine, or 1 additional cup prepared low-sodium beef broth
1 can (28 ounces) crushed tomatoes
1½ cups prepared low-sodium beef broth, plus a little extra only if needed during braising
¾ teaspoon dried thyme, or 3 fresh thyme sprigs
3 dried bay leaves
1 pound (16 ounces / 454 grams) dry penne
Water for boiling the pasta, with salt to taste; reserve 1 cup pasta cooking water before draining
Instructions
Heat the oven to 325°F. Pat the beef dry and season it with 1 teaspoon of the measured sea salt and all the pepper. Heat 2 tablespoons of the olive oil in a heavy 6-quart oven-safe pot over medium-high heat. Brown the beef in 2 batches, about 3–4 minutes on each broad side; it does not need to be cooked through at this stage. Transfer to a clean plate.
Reduce the heat to medium and add the remaining 1 tablespoon oil. Cook the onion, carrots and celery for about 7–10 minutes, stirring, until the onion softens. Add the garlic and cook for 30 seconds. Stir in the tomato paste and cook for 1–2 minutes.
Pour in the cup of red wine, or its separate 1-cup broth alternative, and scrape up the browned bits. Simmer for about 3–5 minutes. Add the crushed tomatoes, the separate 1½ cups prepared broth, thyme, bay leaves and remaining ½ teaspoon sea salt. Stir, then return the beef and any juices to the pot. The liquid should come well up the sides of the beef; it need not cover it completely.
Bring to a gentle simmer, cover tightly and put the pot in the oven. Braise for about 2½–3½ hours, turning the pieces and checking the liquid every 45–60 minutes. Keep a little liquid around the meat; if the sauce becomes dry before the beef is tender, add a small splash of the extra prepared broth. The beef is ready when a fork twists through it easily and the pieces pull apart without resistance. Keep cooking in 20–30-minute intervals if still firm.
Transfer the beef to a clean board. Discard the bay leaves and any woody fresh thyme stems. Shred the meat with 2 forks, removing any large remaining fatty pieces. Return the shredded beef to the sauce. If the sauce is thin, simmer uncovered on the stove for about 10–20 minutes, stirring, until it coats the meat. Keep warm over low heat.
While finishing the sauce, cook the pound of penne in a large pot of water, salted to taste, until al dente according to its package. Reserve 1 cup cooking water and drain. Toss the full sauce batch with the pasta in the roomy pasta pot, adding the reserved pasta water a little at a time only as needed so the sauce coats the penne. Heat together gently for about 1–2 minutes and serve. If saving some sauce for another meal, set that portion aside before tossing and cook less pasta for the current meal.
Refrigerate leftovers promptly in shallow containers, within 2 hours or within 1 hour above 90°F, and use within 3–4 days. The sauce can be frozen separately for up to 3 months; cool it promptly in the refrigerator before freezing. Thaw in the refrigerator and reheat to 165°F throughout before tossing with freshly cooked pasta.