Heat oil in a 12-inch skillet over medium heat until shimmering. Add onion, thyme, tomato paste, garlic, anchovy, and red pepper flakes and cook until onion is softened and lightly browned. Stir in flour and cook for 1 minute. Slowly whisk in vinegar, scraping up any browned bits and smoothing out any lumps; cook until slightly reduced, about 3 minutes, and transfer to a slow cooker.