**Ingredients**
– 1 (3-pound) boneless beef chuck roast, trimmed
– 3 teaspoons kosher salt, divided
– 1 teaspoon freshly ground black pepper, divided
– 3 tablespoons olive oil, divided
– 6 large yellow onions, thinly sliced (about 12 cups)
– 4 cloves garlic, minced
– 3 tablespoons all-purpose flour
– 1 cup dry red wine
– 2 1/2 cups low-sodium beef broth
– 5 sprigs fresh thyme, plus more for serving
– 2 dried bay leaves
**Instructions**
1. **Prepare the Roast**: Pat the beef chuck roast dry with paper towels, then season it all over with 2 teaspoons of kosher salt and 1/2 teaspoon of black pepper.
2. **Sear the Roast**: Heat 1 tablespoon of olive oil in a large Dutch oven over medium-high heat until shimmering. Add the roast and sear for 4 to 5 minutes per side, until dark golden-brown on two sides. Transfer the roast to a large plate.
3. **Cook the Onions**: Reduce heat to medium and add the remaining 2 tablespoons olive oil to the pot. Add the sliced onions, remaining 1 teaspoon kosher salt, and remaining 1/2 teaspoon black pepper. Stir well, then cover and cook undisturbed for 5 minutes. Stir, cover again, and cook another 5 minutes.
4. **Caramelize the Onions**: Uncover and continue cooking the onions, stirring occasionally, until they become a rich caramel brown color (about 30-40 minutes). Scrape the bottom of the pot as needed to prevent burning. Adjust the heat if necessary. Preheat the oven to 325°F with a rack in the lower third.
5. **Add Garlic and Flour**: Stir in the minced garlic and cook for 1 minute. Sprinkle the flour over the onions, stir well, and cook for another minute.
6. **Deglaze and Simmer**: Pour in the red wine, stirring to scrape up the browned bits from the pot. Add the beef broth, thyme sprigs, and bay leaves, stirring to combine.
7. **Return the Roast and Braise**: Place the roast (with any juices) back in the pot and bring to a simmer. Cover and transfer to the preheated oven. Cook for 3 to 3 1/2 hours, until the meat is tender and falls apart easily when pricked with a fork.
8. **Finish and Serve**: Skim off excess fat if desired. Remove and discard thyme stems. Use tongs to shred the roast into bite-sized pieces directly in the pot. Garnish with additional fresh thyme leaves, if desired, and serve warm.