Sauté onion in butter in a large Dutch oven 25 minutes or until tender. Stir in flour and salt. Add water and bouillon cubes, stirring well. Bring mixture to a boil. Reduce heat; cover and simmer 30 to 40 minutes. Gradually add 1 quart milk, stirring well. Heat thoroughly (do not boil).
Place soup in ovenproof bowls. Top each with 1 croûte and 1/4 cup cheese. Bake at 325° for 5 minutes or until cheese melts. Serve immediately.