In a large nonstick skillet, heat oil over medium heat. Add onions, thyme, and 1 Tablespoon of water. Cover; cook for 5 minutes. Uncover; reduce heat to medium low. Cook until onions are golden, stirring, about 15 minutes. Add garlic; saute for 1 minute. Add the flour; reduce heat to medium. Cook; stirring for 2 minutes. Stir in the broth, remaining water and nutmeg. Bring to a boil; skim off foam. Reduce heat to low; cover and simmer for 30 minutes. Preheat broiler. Place 2 heat proof bowls on a baking sheet; ladle soup into bowls. Top each with a slice of toast; sprinkle with Swiss cheese and Parmesan. Broil until cheese is bubbly, about 1 minute. Serve immediately.
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