Trim fat from brisket. Place onion in a large Dutch oven; top with meat. Arrange orange slices over meat. Combine juice and next 6 ingredients, stirring well. Pour mixture over meat. Bring to a boil; cover, reduce heat, and simmer 1 1/2 hours.
Add carrot, potato, and apple to Dutch oven; cover and cook 30 minutes or until carrot and potato are tender. Add prunes; cook 15 additional minutes.
Transfer meat and vegetable mixture to a serving platter, using a slotted spoon; set aside, and keep warm.
Skim fat from broth in Dutch oven. Add flour to broth, stirring until smooth. Cook over medium heat, stirring constantly, until thickened.
Cut meat diagonally across grain into 1/4-inch-thick slices. Serve meat and vegetable mixture with gravy.