Pat 3 pounds cubed boneless beef chuck dry with paper towels. Season all over with 2 teaspoons of the kosher salt and ½ teaspoon of the black pepper.

Heat 1 tablespoon of the vegetable oil in a broiler-safe Dutch oven over medium-high heat until shimmering. Add half of the beef and sear until browned on two sides, 2 to 3 minutes per side. Transfer the beef to a plate. Add 1 tablespoon of the vegetable oil to the pot and repeat searing the remaining beef. Reduce the heat as needed if the fond on the bottom of the pot becomes too dark or starts to burn. Transfer the second batch of beef to the plate.

Reduce the heat to medium. Add the remaining 2 tablespoons vegetable oil, 2 pounds sliced yellow onions, 5 fresh thyme sprigs, 2 dried bay leaves, the remaining 1 teaspoon kosher salt, and remaining ½ teaspoon 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.

Reduce the heat to medium-low, uncover and continue to cook, stirring occasionally at first and then more frequently once the onions start to brown, scraping the bottom of the pot when stirring, until the onions are a rich caramel brown color, 15 to 20 minutes. Reduce the heat as needed if the bottom of the pot is getting too dark. Remove and discard the thyme stems.

Stir in 4 minced garlic cloves and 3 tablespoons all-purpose flour, and cook until the garlic is fragrant, about 1 minute. Add 3 ½ cups beef broth, and return the beef and any accumulated juices to the pot. Stir to combine and bring to a boil over medium-high heat.

Reduce the heat to medium-low to maintain a simmer. Cover and cook, stirring every 20 minutes or so, for 1 hour. Stir in 8 ounces quartered cremini mushrooms and cook uncovered until the beef is very tender and the sauce thickens, 1 hour to 1 hour and 15 minutes. About 15 minutes before the stew is ready, heat the oven to broil.

Stir 1 teaspoon sherry vinegar into the stew. Taste and season with more kosher salt or black pepper as needed. Remove and discard the thyme stems and bay leaves.

Sprinkle the stew evenly with 6 ounces shredded Gruyère cheese. Transfer to the oven and broil until the cheese is melted and browned in spots, 3 to 5 minutes.

Serve the stew with mashed potatoes or crusty bread, garnished with more fresh thyme leaves and black pepper.