Arrange the bouquet garni herbs so that they're in an even pile. Use some butcher's twine to tie the bundle together around the center. Set aside.
Dry the chuck roast pieces with a paper towel. Season all over with salt and pepper.
Place a Dutch oven (or a large pot, at least 3 quarts) over high heat. Add the olive oil, and once hot, brown the beef pieces on all sides. Do not overcrowd the pot. You will need to work in batches to get a good sear.
Add all the beef back to the pot and sprinkle with flour. Stir to coat the beef and let that cook for 1 minute.
Pour a generous amount of red wine into the pot to deglaze. Stir and let reduce for 1-2 minutes. Add more wine, stir, and reduce again. Continue until the flour dissolves and the sauce becomes creamy.
Add the beef broth, 1 teaspoon salt, and bouquet garni to the pot. Cover and reduce the heat to medium-low. Simmer for about 2 hours or until the meat is tender.
When there is about 30 minutes of cooking time left for the beef, place a large skillet over medium-high heat. Add the bacon and shallot and cook until they are browned and slightly crisp.
Add the garlic, mushrooms, and carrots. Cover the skillet and braise for 20 minutes.
Once the beef is done, remove the bouquet garni with tongs or a fork. Add the bacon & vegetable mixture to the pot and stir everything together. Season with salt and pepper to taste.
Portion into bowls and serve as a stew or serve over mashed potatoes. Garnish with more fresh thyme if desired.
Notes
If you prefer, you may substitute pearl onions for shallots.
If you can't find fresh bay leaves at the store, you can use 2 dried leaves instead. Just be sure to remove them when you take out the bouquet garni.