Start by peeling the papery skin off of the shallots and separating the bulbs. Slice the tips and roots off of the shallots, leaving the stems intact. If the shallots are large, cut them in half length-wise.

Working one at a time, turn a shallot onto the flattest side (this will keep it stable). Then, cut the shallot length-wise into thin slices, about 1/8-1/4-inch thick.

One the shallot is too thin to slice comfortably, flip it sideways onto the flat side. Then, thinly slice the rest of the shallot. Repeat with the remaining shallots and set aside.

Start by melting the butter in a large Dutch oven over medium-low heat. Then, add the sliced shallots and a few generous pinches of salt.

Cook the shallots, stirring often, until they're soft and translucent. If the shallots start to stick to the pan, add a few drops of water to loosen them up. Continue cooking the shallots, stirring every couple of minutes so they don't stick to the pan or brown too much in one place. After about 20 minutes, the shallots will be blonde-colored. If they're browning too much or sticking a lot, reduce the heat.

Keep cooking the shallots, low and slow, until they're deep brown and caramelized, another 25-35 minutes. If they're not a deep brown, keep cooking for another 10-30 minutes. Stir the shallots often so they don't burn or stick to the pan. Be patient! This process can take anywhere from 45 minutes to 1 1/2 hours total depending on the pan and heat source.

Once the shallots are caramelized, increase the heat to medium high. Add the garlic and cook for 1 minute until the garlic is softened and fragrant. Deglaze the shallots with the white wine, scraping up any brown bits on the bottom of the pot. Let the wine simmer until it's almost completely evaporated and the onions are jammy.

Stir in the flour and cook for about 1 minute. Add the beef broth, black pepper, thyme, and a bay leaf. Bring the soup to a boil. Then, reduce the soup to a gentle simmer and let it bubble on the stove for about 30 minutes, until it's rich and glossy. Remove the thyme stems and bay leaf and discard. Taste the soup and add more salt and pepper if needed.

Set the broiler on high and place an oven rack about 6 inches away from the broiler. Slice the bread into 12-18 slices (about 1/2-inch thick) and line them on a sheet pan. Broil the bread slices until they're lightly toasted, about 2-3 minutes per side.

Meanwhile, combine the gruyère cheese and parmesan cheese in a small bowl. Evenly divide the cheese between the tops of the croutons. Broil for another 2-4 minutes until the cheese is melted and bubbling.

Ladle the soup evenly between 6 bowls. Top each bowl of soup with one gruyère crouton and sprinkle the tops generously with fresh chives. Serve extra croutons on the side for dipping. Enjoy!