Preheat oven to 325 degrees. 

Generously season the short ribs with fresh cracked pepper and Kosher salt, rubbing it over all sides. Heat the oil in a large dutch oven over medium high heat. Add the short ribs to the pan in a single layer and sear, leaving the ribs in place for several minutes before turning. Repeat on all sides. Remove the short ribs to a plate. 

Drain off any excess fat from the pan, leaving 1 Tablespoon in the pan. Lower the heat to medium. Add the onions and saute until softened, 5-7 minutes. Add the garlic and saute an additional minute, until fragrant. Pour in the wine and use a wooden spoon or spatula to scrape up any browned bits from the bottom of the pan. Bring to a simmer and cook for an additional 5 minutes, or until reduced slightly. 

Nestle the short ribs back in the pan, then pour in the beef broth. They should be just barely covered. Place the rosemary, thyme, and bay leaf in the liquid surrounding the beef. 

Cover the pot and place in the oven. Bake for 2 1/2 to 3 hours or until beef is very tender. Remove from the oven and allow to rest before serving.

Optional but recommended: Place the pot in the fridge overnight. When you're ready to reheat, scrape off the hard layer of fat on top and discard. Reheat the beef in a 400 degree oven for 15-20 minutes or on the stove top over low heat. I recommend serving the beef with the liquid and onions over mashed potatoes, polenta, or egg noodles.