Melt the butter in a large stockpot over medium-high heat, Add the chopped onions and salt and sauté for about 20 minutes, or until the onions are golden brown.
Add 1 tablespoon of flour, stir to coat the onions, and sauté for another minute, until the flour becomes fragrant like pie crust.
Add the beef stock, chicken stock, beef base, and thyme. Reduce the heat to low and simmer for 15 to 20 minutes.
Serve topped with croutons and shredded Gruyère and Asiago cheese.