Preheat an oven to 325°F. Pat the short ribs dry with a paper towel and season all over with salt and pepper.
Add the oil to a dutch oven on medium-high heat. Once the oil is hot, sear the beef on all sides until browned. You may need to do this in batches. Remove the beef from the pan.
Decrease the heat to medium and add the butter. Add the diced onions, celery, and carrots to the pot and saute for 6-8 minutes, while stirring occasionally. You really want the veggies to brown a bit. Add the garlic and cook for another minute.
Add the tomato paste to the veggies and stir well. Cook for 3-4 minutes, until the tomato paste has darkened in color a bit. Sprinkle in the flour, stir, and cook for another 2-3 minutes.
In a large measuring cup, whisk together the red wine, dijon, and beef stock. Season the sauce with salt and pepper, then pour it into the pot and stir well so that there aren't any clumps of flour. Bring the liquid to a gentle simmer.
Nestle the short ribs into the pot. It should reach about ¾ of the way up the short ribs. Tie the thyme and rosemary into a bundle with kitchen twine and nestle them in the middle of the meat. Tuck the bay leaves into the sauce around the short ribs. Cover and transfer to the oven.
Braise for 2 ½- 3 hours, until the beef is very tender. Remove from the oven and let it rest covered for 30 minutes.
Season the short ribs to taste with additional salt and pepper. Discard the herbs and serve the red wine braised short ribs drizzled with the braising liquid over mashed potatoes, risotto, or polenta.