Preheat oven to 325°F.

Heat olive oil in a heavy ovenproof pot (like a Dutch oven) over medium high heat.

Season flour with a little salt and pepper, mix it with your fingers and dredge the short ribs in the flour. Shake off the excess flour and set aside.

When the oil is hot, carefully add the ribs to the pot and brown on both sides. (You may have to do this in two batches; you don't want to crowd them or they won't brown properly.)

Remove the ribs from the oil and set aside. (This can be done a day ahead if you are pressed for time; cover and refrigerate until ready to braise.)

Wipe out the pot, then add the onions. Reduce heat to medium and cook until softened and beginning to caramelize, about 10 - 12 minutes. Add a pinch of salt and a few turns of the pepper grinder and stir. 

Add the carrots, celery and garlic and cook for 5 more minutes. 

Add apple cider and beef stock to the pot and stir to combine. Put the ribs back into the pot, then add apple, bay leaves, thyme, rosemary and stock. 

Season with a few pinches of salt and a few more turns of the pepper grinder. Place lid on the pot and slide into the oven for 3 - 3 1/2 hours.

Remove the pot from the oven and allow the ribs to cool slightly, uncovered. Remove the ribs and set aside, remove bay leaves, rosemary and thyme, and discard.

Remove vegetables from the pot and pour liquid into a glass measuring cup. Skim the fat from the surface, then puree the braising liquid with 1/4 of the vegetables to make a gravy. (*see note)

Return the short ribs to the pot and serve.