In a Round French Oven, over medium heat, add butter, onions, thyme, bay leaves and salt. Cook uncovered, stirring frequently, until onions are very soft and deep golden brown, about 45 minutes.
Add flour and cook, stirring, 1-2 minutes.
Stir in wine and cook, stirring, 2- 4 minutes.
Add stock, water, and pepper. Simmer, uncovered, stirring occasionally, 30 minutes. Preheat oven to 350°F (176°C).
Arrange bread in a single large on a baking sheet and toast, turning over once, until completely dry, about 15 minutes. Remove bread from oven and preheat broiler.
Discard bay leaves and thyme from soup and divide soup among French Onion Soup Bowls. Place a piece of toasted bread in each bowl.
Divide and sprinkle cheese evenly between soup bowls.
Broil until cheese is melted and bubbly, 1 to 2 minutes.