Mix flour, salt, and pepper in a large plate or shallow, wide glass dish. Cover meat in a light dusting of flour mixture.
Heat the oil in a wide pan over medium-high heat. Working in batches, sear meat on all sides until brown and slightly caramelized. Add additional oil as needed. Remove from pan and set aside.
Add sliced onions to pan and sauté for 8 to 10 minutes, until translucent, scraping up brown bits as you go.
While onions are cooking, combine ketchup, apple cider vinegar, spices, Worcestershire sauce, brown sugar, and 1 cup water or stock in a small bowl. Add this sauce to pan with onions and simmer 1 to 2 minutes.
Add seared meat back to the pan, lower heat to low, and simmer for 2 to 2 1/2 hours, or until meat is tender. Add more water or stock as needed.