Melt 2 tablespoons butter in a large heavy-bottomed pot over medium-low heat. Add sliced onions, garlic, and salt. Cook gently, stirring every 5 to 10 minutes, until deeply golden and caramelized, about 40 to 60 minutes. Add remaining butter halfway through.

Pour in the red wine, scraping up any browned bits from the bottom of the pot. Simmer over medium heat until the wine reduces by half.

Add beef broth, black pepper, and thyme sprigs. Bring to a gentle boil, then reduce heat and simmer uncovered for 1 hour. Season to taste.

While the soup simmers, preheat oven to 350°F (180°C). Toss bread cubes with olive oil, salt, and pepper. Spread on a lined baking sheet and bake 10 to 13 minutes until crisp and golden.

Set oven to broil. Remove thyme sprigs from the soup. Ladle soup into oven-safe bowls, top generously with croutons and Gruyère cheese. Broil 1 to 2 minutes until cheese is melted, bubbly, and golden brown. Serve immediately.