In large ziptop bag, combine the beef, onion, garlic, thyme, black pepper, bay leaves, olive oil and red wine. Seal the bag and refrigerate overnight.

Preheat oven to 300ºF.

Remove the beef from the marinade and dry with paper towels. Season the beef generously with salt and pepper. Reserve the marinade.

In a large Dutch oven over medium-high heat on the top of the stove, add the olive oil and 2 tablespoons of the butter. Add the beef to the Dutch oven, and brown on all sides, about 4-6 minutes per side. Remove the browned bits of meat to a plate. Add the bacon and cook until browned and fat has rendered but not crisp. Add the carrots, and continue to cook until lightly caramelized, then add the tomato paste and cook for an additional minute, while stirring and scraping the bottom of the pot to prevent the tomato paste from burning. Return meat to the pot and sprinkle the flour over the beef and the vegetables. Stir to coat. Cook until the flour is absorbed and lightly browned, about 2 minutes. Add the remaining marinade and beef stock and bring to a simmer. Cover with a lid and bake in the oven for 2-2 1/2 hours, stirring occasionally.

In a medium pan over medium-low heat, add 2 tablespoons of butter and the pearl onions. Season the onions with salt and pepper and continue to cook until lightly brown on all sides, about 8-10 minutes. Then, add the remaining 2 tablespoons of butter, mushrooms and garlic to the pan. Cook until golden brown, about 6-8 minutes. Season with salt and pepper. Remove from heat and set aside until the beef is finished cooking.

Remove the stew from the oven and add the onions and mushrooms to the pot and stir to combine. Season to taste, and allow to sit for 20 minutes before serving. Serve with crusty bread.