Combine the chilis and the hot water in a large pot or bowl, and let stand 20 minutes, or until chiles are softened.
In a blender, combine two quarters of the onion, tomatoes, garlic, thyme, oregano, cumin, ginger, and the chiles and liquid. Process until smooth.
Meanwhile, heat olive oil in a Dutch oven set over medium heat.
Season the beef with salt and pepper.
Add beef to the heated oil and brown on all sides; about 3 to 4 minutes per side.
Add in the bay leaves and remaining onions.
Stir in the blended sauce, and add in the beef broth.
Bring mixture to a boil; reduce heat.
Cover and simmer for 1-½ to 2 hours, or until meat is fall-apart tender.
Remove meat and transfer to a cutting board.
Remove the onions and bay leaves from the pot.
Continue to simmer the liquid, uncovered, until reduced by half; about 20 to 30 minutes.
Shred the meat with forks, and stir back into the pot.
Transfer to a serving bowl or plate.
Garnish with onions and cilantro.
Serve in warm tortillas, over rice, or as a filling for tacos, burritos, quesadillas, and more.