In a glass bowl, combine onion, tomato, parsley, thyme, rosemary, ginger, cinnamon and lime juice. Add chicken, turning to coat evenly. Cover and refrigerate for 2 hours.
Remove chicken from marinade, discarding marinade. Place chicken in a Dutch oven or pot and add 3 cups (750 mL) water, salt and pepper. Cover and bring to a boil over high heat. Reduce heat to low and simmer for 1 1/2 hours or until chicken is tender.
In a small saucepan, heat oil over medium heat. Stir in flour and nutmeg until blended. Remove 1 1/2 cups (375 mL) liquid from stew and strain. Gradually stir into flour mixture and cook, stirring, for about 2 minutes or until thickened.
Place chicken pieces on a warm platter. Serve drizzled with sauce. (Strain remaining liquid from stew for later use.)