In a large stockpot, cook the onions, garlic, salt and pepper over medium heat until the onions get super soft and take a beautiful caramel color, about 20-25 minutes. Stir often so the onions don't burn.
When the onions are ready, add nutmeg, star anise, juniper berries, bay leaf, dried savory, Dijon mustard and stock.
Bring to a boil then cover, lower the heat and simmer for 20-25 minutes to allow the flavors to infuse. Turn off the heat and remove bay leaf, star anise and juniper berries.
When you are ready to serve the soup, ladle it into 4 oven safe individual soup bowls and place a piece of stale bread in each bowl. You want your bread to be on the very dry side. If you find it's not dry enough, give it a few minutes in the toaster.
Mix all the cheeses together and sprinkle evenly over the 4 bowls.
Place the bowls in a 375F oven and cook until the cheese is all melted and bubbly and turns a beautiful golden color. (you might want to place a cookie sheet or piece of aluminum foil underneath to catch possible overspillage)
Notes
*I made my own stock by throwing my turkey carcass along with everything that was in it (apples, oranges and sage) in enough water to cover all and I let that simmer for about 2 hours. I then strained my stock and put it in the fridge to cool completely, which made removing the very thin layer of fat that solidified on the surface super easy.Mayo Clinic also has an excellent recipe for low fat chicken stock. You can use the same method to make turkey stock.