Arrange a rack in center of oven; preheat to 325°. Pat beef dry with paper towels. Pulse or crush onion soup mix, pepper, and 1 Tbsp. salt until large pieces are broken down. Season beef all over with seasoning mix.
In a large skillet over medium heat, heat 1 Tbsp. oil. Cook beef until just starting to brown, 3 to 4 minutes per side. Transfer to a plate.
In the same skillet, heat remaining 1 Tbsp. oil. Add onions; season with remaining ½ tsp. salt. Cook, stirring occasionally, until onions start to brown, about 10 minutes. Add wine and cook until liquid is slightly reduced, 2 to 3 minutes. Pour in broth and return beef to skillet. Add thyme and bring to a simmer. Cover and transfer to oven.
Roast beef, turning halfway through, until meat easily pulls apart with a fork, 2 hours and 45 minutes to 3 hours.
Transfer beef to a cutting board. Remove and discard thyme. Return skillet to medium heat and bring sauce to a simmer. Cook until liquid is reduced by about half, about 15 minutes. Shred beef into large pieces and return to skillet.
Heat broiler to high. Top skillet with cheese. Broil until cheese is melted and starting to brown in spots, about 5 minutes.
Top with more thyme. Serve with sliced baguette alongside.