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Pre-heat a large sauté pan over medium heat.
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Add the olive oil to the hot pan and add the onions. Cover the onions with the parchment paper circle. (This is not essential, but it helps prevent the onions from drying out.) Let the onions start to brown a little and then give them a good stir, scraping the bottom of the pan. The trick is in how often to stir – if you stir too much, the onions won’t get a chance to brown; if you don’t stir often enough, the onions might start to burn.
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As the onions start to brown more uniformly, season the onions with salt. The salt will draw out some of the moisture from the onions, which will then pick up the browning on the bottom of sauté pan and mix in with the onions.
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If the pan starts to get too brown, add a little water or white wine to the pan and stir.
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Continue to cook the onions like this for about 30 minutes until the onions are a deep golden brown.
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Deglaze the pan with white wine, scraping up all the brown bits on the pan. Add the beef stock, sprigs of thyme and bay leaves. Simmer for 30 minutes.
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Slice the baguette into 2-inch slices. Toast the baguette slice in a 350ºF oven until they are crisp and lightly browned. Gently rub the garlic clove over the toasted bread.
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Season the soup with salt and freshly ground black pepper to taste. Finish by stirring in the butter.
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When you are ready to serve, pre-heat the broiler to high. Ladle the soup into oven-safe bowls or crocks. Add about a ½ teaspoon of brandy or sherry to each bowl. Top with 1 or 2 toasted baguette slices and sprinkle the Gruyère cheese on top to cover the soup and bread.
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Place the bowls or crocks on a sheet pan and place under the broiler until cheese is browned and melted. Garnish with fresh thyme leaves and serve immediately.