Melt butter over medium heat and add onions, garlic, thyme, and bay leaves. Cook until onions caramelize, about 25 minutes.
Add wine and simmer until onions are dry, about 10 minutes. Remove bay leaves.
Sprinkle onions with flour and reduce heat to medium low and cook for about 5 minutes until flour is browned.
Add beef bouillon and water and bring to boil and simmer for about 1-2 hours.
When ready to eat, heat broiler and ladle soup into a crock and add hard crusty french bread hunks to soup. Placed sliced Gruyere to top and place close to broiler for 1-2 minutes until cheese is golden brown.