To make the Brisket: preheat the oven to 325 degrees F.
Fill a small saucepan with water, and bring to a boil over high heat. Add the garlic, bring back to a boil, and cook rapidly until slightly softened, about 1 minute. Use a slotted spoon to transfer the garlic to a bowl of ice water. Peel when cool enough to handle.
Combine the flour, salt, and pepper in a large shallow dish or large platter. Add the brisket and turn to coat on all sides. Shake off the excess. Heat the oil in a large covered casserole or Dutch oven over medium-high heat until almost smoking. Add the brisket and cook, turning often, until well browned, about 6 to 8 minutes per side. Transfer to a plate or platter and pour off all but 2 tablespoons of the fat. Stir in the onions and the peeled garlic. Reduce the heat to medium and cook, stirring often, until golden, about 10 minutes. Pour in the wine and stir to pick up any browned bits on the bottom of the casserole. Stir in the tomato paste and add the bay leaves and thyme. Increase the heat to high and bring to a boil. Cook rapidly, stirring often, until almost all the liquid has evaporated. Pour in the stock and bring back to a boil. Reduce the heat to medium and add the brisket. Cover tightly with a piece of foil, then cover the pot with the lid. Transfer to the lower third of the oven and cook until a fork comes out easily when pierced, 3 to 4 hours.
To make the Horseradish Sauce: mix the horseradish, vinegar, mayonnaise, chives, and lemon juice in a small bowl. Stir well to blend and season with salt and pepper. You should have about 1 cup. Keep refrigerated until ready to serve.
To make the Disks: whisk the stock, eggs, and margarine together in a small bowl. Stir in the salt and matzo meal to form a soft dough. Cover with plastic wrap and refrigerate until well-chilled, about 1 hour. Bring a large pot of salted water to a boil over high heat. Working with 1 tablespoon of dough at a time, use wet hands to form the dough into disks about 1 1/2 inches wide and 1/2-inch thick. You should have about 18 disks. Drop them into the boiling water and reduce the heat to medium-low. Cover and simmer until the disks are puffy and cooked through, 30 to 35 minutes.
Transfer the brisket from the casserole to a cutting surface and cover loosely with foil. Let rest for 15 minutes. Gently skim the surface of the liquid in the casserole with a spoon to remove as much fat as possible. Remove and discard the bay leaves. Add the disks to the cooking liquid and cook on top of the stove over medium heat, covered, until they've turned dark and absorbed some of the sauce, about 10 minutes.
Thinly slice the brisket on an angle, cutting against the grain. Arrange the slices on a warmed serving platter or plate and spoon on some of the horseradish cream. Place the disks on the side and ladle on the pan gravy. Serve warm.
A Brisket Primer: You can buy beef brisket 3 ways: 1. Whole with deckle (the deckle is a thin layer of meat with a lot of connective tissue and fat that lies on the underside of the brisket; it can be removed easily), weight in at 8 to 10 pounds. If you remove the deckle, the remaining piece of brisket weighs 7 to 8 pounds. 2. Flat cut, also known as the first cut or thin cut. This is the leanest of the possibilities and the most popular, and it usually weighs around 4 pounds. 3. Point cut, cheaper and fattier than the flat cut, also 4 to 5 pounds.