In a blender, combine the chipotles with adobo sauce, garlic, cumin, oregano, ground cloves, apple cider vinegar, lime juice, and salt. Blend until smooth.
Place the sliced onion and bay leaves in the bottom of the slow cooker. Set the chuck roast on top.
Pour the chipotle paste over the meat, then add the beef broth.
Cover and cook on low for 8-10 hours or high for 5-6 hours, until the beef is fork-tender.
Remove the beef and shred it with two forks. Discard the bay leaves.
Return the shredded beef to the slow cooker and stir it into the juices. Serve in tacos, burritos, or bowls.