Preheat the oven to 325°F.
Cut the chuck roast into 2-3 inch cubes and season with salt and black pepper.
Heat avocado oil in a large Dutch oven over medium-high heat. Brown the beef in batches on all sides. Transfer the browned beef to a plate and set aside.
Reduce the heat to medium. Add the diced onion and whole garlic cloves to the Dutch oven. Sauté until the onions are translucent.
Add the chipotle pepper, adobo sauce, and tomato paste. Stir and cook for 1-2 minutes, allowing the tomato paste to darken slightly.
Return the browned beef and accumulated juices to the Dutch oven. Sprinkle with flour and stir to coat. Cook for 1-2 minutes.
Pour in the beef broth and scrape the bottom of the Dutch oven to release the browned bits.
Bring to a simmer. Add the cloves, cinnamon stick, cumin, allspice, bay leaves, chocolate, and lime juice. Stir until the chocolate is incorporated.
Cover the Dutch oven with a tight-fitting lid and transfer to the preheated oven.
Braise at 325°F for approximately 1½-2½ hours, or until the beef shreds easily with a fork. Check the liquid level during cooking and add a little broth if needed.
Remove the whole spices. Shred the beef with two forks and stir into the sauce before serving.