Preheat an oven to 350 F.
Prep the beef and onions. Cut the beef into 2-inch cubes and season them well with salt and pepper and set them aside. Peel the onions and cut them in half, root to stem. Use a mandoline to thinly slice them to about 1mm. If you’re great with a knife, you can definitely do it by hand, but a mandoline will ensure that all the onion slices are even and that they’ll cook evenly and melt into the sauce. Use a piece of kitchen twine to tie the thyme sprigs into a bundle.
Sear the beef. Heat the oil in a 5-quart Dutch oven over medium heat.. Pat the beef pieces dry with a paper towel and season liberally all over with salt and pepper. Arrange the beef pieces in a single layer in the dutch oven (you may need to do this in batches) and sear the beef for 4-5 minutes per side until it’s deeply browned. Transfer the beef to a plate.
Caramelize the onions. After removing the beef, add butter to the dutch oven and reduce the heat to medium-low. Add in the onions and toss well to coat in the butter. Cover with a lid for 5 minutes. Uncover, add the sliced garlic, and continue to cook, stirring occasionally, until the onions are deeply caramelized, about 30-40 minutes.
Build the sauce and braise. Once the onions are caramelized, stir in the Worcestershire, dijon, and flour. Stir in the vermouth and bring to a simmer for 5 minutes. Stir in the beef stock and season with salt and pepper. Add the beef back to the pot with the bay leaves and the thyme bundle. Cover and transfer to the oven for 3 hours, or until the beef is tender and easily shredded. Remove from the oven and let the beef rest for 15 minutes.
Toast the baguette. While the beef rests, lay the sliced baguette on a baking sheet and drizzle with the olive oil. Toast in the oven for 8-10 minutes, until golden brown and crisp. Remove the sheet from the oven and set the broiler on high.
Finish the braised beef. Discard the bay leaves and thyme bundle from the beef stew. Lay the toasted baguette slices over the top of the beef stew and top with the shredded gruyere cheese and thyme leaves and a crack or two of black pepper. Transfer to the oven under the broiler for 3-4 minutes, until the cheese is browned and bubbling. Serve right away.