On a large plate mix together flour, salt and pepper.
Coat the short ribs one at a time in the flour mixture.
Heat the olive oil in a large heavy pot over medium heat, when hot add the ribs and cook on all sides until well browned, then transfer to a plate.
Add the onions, carrot, celery, and garlic to the pot, and cook until the vegetables begin to soften, about 5 minutes.
Add the tomato paste, wine, and bring to a boil.
Reduced the wine by half, add the chopped tomatoes, beef broth, red pepper flakes, bay leaves, oregano, rosemary, and parsley.
Bring mixture to a boil then add the ribs back into the pot; reduce to a simmer and cover.
Simmer until the meat is very tender, about 2 to 2 1/2 hours.
To prepare the gremolata: place the parsley, garlic, and lemon zest on a cutting board and chop together.
When the meat has cooked, skim fat off the top, and remove the rosemary sprigs and bay leaves.
Sprinkle the plates with the gremolata and and place the short ribs with the sauce in the center.
This is delicious served over mash potatoes.