Heat a large Dutch oven over medium-high heat. Coat pan with cooking spray. Add 1/4 teaspoon salt and beef to pan; cook 6 minutes or until browned, stirring to crumble. Transfer beef to a small bowl; keep warm.
Reduce heat to medium; recoat pan with cooking spray. Add 1 1/2 cups onion to pan; cook 4 minutes, stirring frequently. Add garlic to pan; cook 1 minute, stirring constantly. Add remaining 1/4 teaspoon salt, oil, and the next 4 ingredients (through nutmeg) to pan; cook 1 minute or until fragrant, stirring constantly. Add tomato paste; cook 1 minute. Add 1 cup water, vinegar, and tomatoes to pan; bring to a boil. Reserve 1/2 cup dark red kidney beans. Add beef, remaining dark red kidney beans, and light red kidney beans to pan; cover, reduce heat, and simmer 30 minutes. Ladle 1 1/4 cups chili into each of 8 bowls. Top each serving with 1 tablespoon remaining dark red kidney beans, about 1 teaspoon remaining chopped onion, and 1 tablespoon parsley.
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