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

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

Reduce heat to medium. Add the remaining olive oil, onions, kosher salt, and black pepper to the pot. Stir well to combine. Cover and cook undisturbed for 5 minutes. Uncover, stir, cover again, and cook for 5 minutes more.

Uncover and continue to cook, stirring occasionally and then more frequently until the onions are a rich caramel brown color, 30 to 40 minutes.

Stir in garlic and cook for 1 minute. Sprinkle flour over the onions, stir well, and cook for 1 minute.

Stir in wine, scraping up the browned bits, then add beef broth, thyme, and bay leaves.

Return the roast and any accumulated juices to the pot and bring to a simmer. Cover and transfer to the oven. Cook until meat is gently falling apart, 3 to 3 ½ hours.

Skim off fat if desired. Remove and discard thyme stems. Shred roast into bite-size pieces before serving. Garnish with fresh thyme leaves if desired.