Heat the oil over medium heat. Add onions and salt, cook for 10 minutes, stirring occasionally.
Add mustard and thyme, stir well, cover, and turn down heat very low. Let the onions simmer in their own juices for 35 minutes.
Add stock, soy sauce, wine, and pepper. Simmer for another 10 minutes.
Ladle the soup into bowls and top with croutons and cheese. If your bowls are oven-proof, you can then place the dishes under the broiler for a minute or two to melt and brown the cheese.