Season the short ribs with 1 tablespoon thyme and the cracked black pepper. Use your hands to coat the meat well. Cover, and refrigerate overnight.

Take the short ribs out of the refrigerator an hour before cooking, to come to room temperature. After 30 minutes, season them generously on all sides with salt.

When you take the ribs out of the refrigerator, preheat the oven to 425°F.

Toss the pearl onions with 2 tablespoons olive oil, 1 teaspoon thyme, ¾ teaspoon salt, and a pinch of pepper. Spread them on a baking sheet and roast them about 15 minutes, until tender. When they have cooled, slip off the skins with your fingers and set aside. Turn the oven down to 325°F.

When it’s time to cook the short ribs, heat a large sauté pan over high heat for 3 minutes. Pour in 3 tablespoons olive oil, and wait a minute or two, until the pan is very hot and almost smoking. Place the short ribs in the pan, and sear until they are nicely browned on all three meaty sides. Depending on the size of your pan, you might have to sear the meat in batches. Do not crowd the meat or get lazy or rushed at this step; it will take at least 15 minutes. When the ribs are nicely browned, transfer them to a braising pan. They should lie flat, bones standing up, in one layer.

Turn the heat down to medium, and add the onion, carrot, celery, thyme sprigs, and bay leaves. Stir with a wooden spoon, scraping up all the crusty bits in the pan. Cook 6 to 8 minutes, until the vegetables just begin to caramelize. Add the balsamic vinegar, port, and red wine. Turn the heat up to high, and reduce the liquid by half.

Add the stock and bring to a boil. Pour the liquid over the short ribs, scraping any vegetables that have fallen on the ribs back into the liquid. The stock mixture should almost cover the ribs. Tuck the parsley sprigs in and around the meat. Cover tightly with aluminum foil and a tight-fitting lid if you have one. Braise in the oven for about 3 hours.

To check the meat for doneness, remove the lid and foil, being careful of the escaping steam, and pierce a short rib with a paring knife. When the meat is done, it will yield easily to a knife. Taste a piece if you are not sure.

Let the ribs rest 10 minutes in their juices, and then transfer them to a baking sheet.

Turn the oven up to 400°F.

Place the short ribs in the oven for 10 to 15 minutes, to brown.

Strain the broth into a saucepan, pressing down on the vegetables with a ladle to extract all the juices. Skim the fat from the sauce and, if the broth seems thin, reduce it over medium-high heat to thicken slightly. Taste for seasoning.

Heat a large sauté pan over high heat for 2 minutes. Tear the Swiss chard into large pieces. Add 3 tablespoons olive oil to the pan, and stir in the cooked pearl onions. Add half the Swiss chard, and cook a minute or two, stirring the greens in the oil to help them wilt. Add a splash of water and the second half of the greens. Season with a heaping a teaspoon salt and a pinch of ground black pepper. Cook for a few more minutes, stirring frequently, until the greens are tender.

Place the Swiss chard on a large warm platter, and arrange the short ribs on top. Spoon lots of braising juices over the ribs. Serve the hot potato purée and horseradish cream on the side.

Potato Puree:

Place the potatoes, whole and unpeeled, in a large sauce pot. Add 2 tablespoons salt and fill the pot with cold water. Bring the potatoes to a boil over high heat, turn down the heat to low, and simmer about 45 minutes, until tender. One type of potato may be done before the other, so check doneness and remove one variety first, if necessary.

When the potatoes are cooked through, strain them, and set them aside to cool for 10 minutes or so. Heat the cream and milk together in a small saucepan, then turn off the heat. When the potatoes have cooled, peel them and pass them through a food mill or potato ricer. Put the riced potatoes in a heavy-bottomed pan. Heat them over medium heat a few minutes, stirring continuously with a wooden spoon, to dry them out a little. Add the butter slowly, stirring constantly. Season with 2½ teaspoons salt.

When all the butter has been incorporated, slowly stir in the warm cream mixture until you have a smooth purée. Taste for seasoning. Pass the purée through a fine-mesh tamis twice if you like.

Horseradish Cream:

Combine the crème fraîche and horseradish in a small bowl. Season with ½ teaspoon salt and pepper. Taste for balance and seasoning.