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In a large pot or dutch oven, melt the butter with 2T oil over low heat. Add the onions and salt. The onions should be almost to the top of your pot, but they will reduce in size considerably. Cover and cook until the onions are very soft, stirring occasionally. Should take about 15 minutes. Then raise the heat to medium-high and cook until the onions are brown, about 10 minutes, stirring to make sure they don't burn. Add the flour and cook for another 2 minutes, stirring to coat.
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Add the wine and use it to scrape the bottom of the pot -- you'll want those bits! Add the stock, thyme, and more salt. Raise the heat to high and bring to boil, then reduce to simmer. Simmer partially covered for 40 minutes.
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While that's simmering, cut the french bread into sizes that will fit your bowls. Heat the broiler. Put bread on a baking sheet, brush with remaining oil, and brown on both sides.
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When soup's done simmering, add the cognac and lots of pepper. Heat the oven to 400°. Place 4-6 oven-proof bowls on a baking sheet and ladle the soup into the bowls. Float the toasted bread in the soup and top with the Gruyère. Bake the soup until the cheese is bubbling, about 10 minutes. You can broil it too if you want it brown. Remove and top with chopped parsley.