Pat the roast dry with paper towels and season with 2 teaspoons kosher salt and ½ teaspoon 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, then transfer to a plate.

Reduce the heat to medium, add remaining olive oil, onions, salt, and pepper to the pot, stir to combine. Cover and cook for 5 minutes, stir, cover again, and cook for 5 more minutes.

Uncover and cook, stirring at first occasionally and more frequently as onions brown, until deeply caramelized, about 30 to 40 minutes. Reduce heat if necessary, scraping bottom of pot when stirring.

Stir in minced garlic and cook for 1 minute. Sprinkle flour over onions, stir well and cook for 1 minute. Add red wine, scraping up browned bits, then stir in beef broth, thyme sprigs, and bay leaves.

Return the roast to the pot and bring to a simmer. Cover and transfer to the oven, cooking until the meat is tender, about 3 to 3.5 hours.

Skim fat if desired, remove thyme stems, and shred the roast in the pot before serving. Garnish with more thyme if desired.