Caramelize the onions: Peel the onions, cut them in half, and then into 1/4-inch (7mm) slices. Heat the clarified butter or butter/olive oil in a large, heavy-bottomed pot over medium heat. When hot add the onions and 1 teaspoon of salt. Cook them for about 45-50 minutes until caramelized - they will be soft and light brown in color. At the beginning you can stir the onions from time to time but as they darken you will need to stir more often. While stirring make sure to scrape all the brown bits on the bottom of the pot. Be careful not to burn the onions - they will be bitter. Anytime the onions look like they are starting to burn on the bottom of the pot - stir them with a spatula or deglaze the pot with a small amount of water.
Add finely chopped garlic and thyme to the pot. Cook for 30 seconds.
Add the wine, cook until it's reduced in volume in 3/4.
Add the broth. Bring to a boil then simmer over low heat for 15 minutes.
While the soup is cooking, make the cheese croutons: Cut the baguette into thick slices and place them on a baking sheet lined with parchment paper. Bake at 425°F (220°C) for 7 minutes or until golden. Top the toasted baguette slices with shredded cheese, bake until melted, about 5 minutes. Set aside.
Add the brandy to the soup. Bring to a boil then immediately take the pot off the heat. Season the soup with salt and pepper.
Assemble: ladle soup into bowls. Sprinkle with a small amount of cheese then put 1-2 slices of baguette in the soup. Sprinkle with thyme leaves and enjoy!