Recipe adapted from The Herbalist’s Healing Kitchen by Devon Young. Used with permission.
1. Toss onions and 1 Tbs. butter in slow cooker. Set heat to low, and cover with lid. Cook about 10 hours, stirring occasionally. (I do not recommend trying to speed up this process by using high heat because it may lead to uneven caramelization.)
2. When onions are cooked, transfer to large stockpot over medium heat. Add flour and 1 Tbs. butter. Cook, stirring, 1–2 minutes to brown the flour.
3. Increase heat to medium-high. Add Cognac, if using, and white wine, and cook 3–4 minutes, until alcohol is mostly cooked off. Add bone broth and thyme, and bring to a low boil. Reduce the heat to medium-low, and cover pot.
4. Preheat oven to 400°F. Melt remaining 2 Tbs. butter, and toss with bread cubes. Place bread on baking sheet, and toast in the oven 15–20 minutes, tossing occasionally to ensure even browning. When golden and crispy, remove the bread from oven. Preheat broiler and place rack close to the heating element.
5. Ladle soup into ovenproof bowls. Top with bread cubes and cheese. Place bowls under the broiler until cheese is melted, bubbly, and slightly browned, 1–2 minutes. Serve immediately.