For the soup:
Add caramelized onions and any juices from the process to a large Dutch oven or pan. Add Brandy, Sherry, Whiskey or Bourbon, heat through. Ignite if you feel comfortable and allow to burn down. Stir in Guinness and cook, stirring frequently, until reduced by half, about 3 or 4 minutes.
Stir in broths, 2 cups water, thyme, and 1/2 teaspoon salt and increase heat to high and bring to simmer. Reduce heat to low, cover, and simmer gently 30 minutes. Remove and discard herbs if whole herbs were used, then season with salt and pepper. Taste for bitterness and add jam or sugar to taste, starting with about 1/4 teaspoon of jam or a pinch or two of sugar. Add more if needed.
For the croutons:
Preheat oven to 400 degrees F.
While soup simmers, remove crust from bread, cut into 1/2″ cubes. Add to the teaspoon and toss with oil. The cubes should all be just coated. Spread to a single ng sheet and bake until bread is dry, crisp, and golden at edges, about 10 to 12 minutes, stirring once or twice and arranging as needed by hand. Set aside.
Adjust oven rack so the top of the croutons are about six inches from broiler element and heat broiler. Set individual broiler-safe crocks on a heavy baking sheet and fill each with about 1 3/4 cups soup, leaving about 1/2″ at the top for the croutons.
Top each bowl with about a tablespoon and a half of cheese, then a layer of croutons. Top with more cheese. Add a few more croutons artfully on top of the first layer and top those with more cheese, taking care to as much as possible, coat the top of the croutons. You’ll be using about 1/2 cup of cheese per serving. See note.
Broil until cheese is melted and bubbly around edges, 3 to 5 minutes. Let cool several minutes before serving. Sprinkle with a little extra thyme if desired.
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