Add onions, carrots, and celery to pot and cook over medium-high heat, stirring often, until onions are browned, about 5 minutes. Add flour and tomato paste; cook, stirring constantly, until well combined and deep red, 2-3 minutes. Stir in wine, then add short ribs with any accumulated juices. Bring to a boil; lower heat to medium and simmer until wine is reduced by half, about 25 minutes. Add all herbs to pot along with garlic. Stir in stock. Bring to a boil, cover, and transfer to oven.