In a large, wide soup pot (at least 4-1/2 qt.), melt the butter over medium heat. Add the onions and season lightly with salt and pepper. (It might seem like you have far too many onions, but they'll cook down to about one-quarter of their original volume.) Cook the onions gently, stirring frequently, until they're very soft and have begun to turn a dark straw color, 35 to 45 min.; I like them when they're still a little toothy and haven't yet begun to brown too much.
When the onions are ready, stir in the flour and cook for 3 to 4 min., stirring frequently. Pour in the wine and increase the heat to medium high, stirring and scraping to loosen any caramelized juices, until the liquid is mostly reduced, 5 to 8 min. Add the broth, toss in the tied herbs, and bring to a simmer. Season to taste with salt and pepper and simmer for 20 to 30 min. to infuse the broth with onion flavor; the onions should be soft but not falling apart. Remove the herb bundle and taste the soup for seasoning. The soup can be made ahead to this point and then cooled and refrigerated for a few days.
To serve -- Heat the oven to 350°F, put the baguette slices on a rack, and toast lightly (7 to 10 min.); set aside. Increase the oven temperature to 450°F. Bring the soup back to a simmer. Set six ovenproof soup crocks on a heavy baking sheet and ladle the soup into the crocks. Float a few toasted baguette slices on top, enough to cover the soup surface without too much overlap. Top the bread with a handful (about 1/4 cup) of the grated Gruyère. Slide the baking sheet into the oven and bake until the cheese is melted and just browning in spots, 10 to 12 min.
Melted, bubbly, just barely golden cheese is what you're after. Serve the soup right away, while the crock is hot and the cheese is still gooey.