Heat the oil in a soup pot. Add the onions and sauté over medium-low heat until golden.
Add the garlic and continue to sauté slowly until the onions are very soft and golden, stirring frequently, about 20 to 25 minutes.
Pour the water over the onions and give them a good stir. Then add the broth, wine, and thyme. Bring to a slow boil, then lower the heat. Cover and simmer gently for 15 minutes.
If using miso, dissolve it in a little warm water, then add to the soup. Or, add soy sauce. Either way, add enough of either to taste. Season with pepper. If time allows, you can let the soup stand off the heat for an hour or two to develop flavor (and will it ever!).
Shortly before serving the soup, cut the bread into ½-inch-thick slices, allowing 1 or 2 slices per serving depending on the size of your soup bowls. Bake at 350 degrees F. for 15 minutes, or until dry and crisp, turning the slices over once about halfway through the baking time. You can also do this in a toaster oven.
Just before serving, sprinkle the bread slices with a generous layer of nondairy cheese. Bake in the oven or toaster oven just until melted.
Reheat the soup if needed, until piping hot.
Ladle into bowls and top each serving with a slice of the bread with melted cheese. As the soup and bread are eaten, another cheese-covered slice can be added to the bowl.