Pat the roast dry with paper towels and season with 2 teaspoons of kosher salt and ½ teaspoon of black pepper.

Heat 1 tablespoon of olive oil in a Dutch oven over medium-high heat. Sear the roast until dark golden-brown on both sides, about 4 to 5 minutes per side. Transfer to a plate.

Reduce heat to medium. Add remaining olive oil, onions, kosher salt, and black pepper. Cook undisturbed for 5 minutes. Stir, cover, and cook for another 5 minutes.

Uncover and cook until onions are caramel brown, 30 to 40 minutes, stirring as needed. Reduce heat if necessary; scrape the bottom of the pot.

Stir in minced garlic and cook for 1 minute. Sprinkle flour over onions, stir, and cook for 1 minute. Add wine and scrape the bottom of the pot. Stir in beef broth, thyme, and bay leaves.

Return roast and juices to the pot. Bring to a simmer, cover, and transfer to the oven. Cook for 3 to 3.5 hours until meat is falling apart.

Skim off fat if desired. Discard thyme stems. Shred roast into pieces in the pot, garnish with thyme if desired.