Step 1Heat the oven to 450 degrees.
Step 2Combine the onions, garlic and shallot in a cast-iron Dutch oven or other very heavy stew pot. They will come up very high and you might think there are too many, but they will cook down quickly. Season the meat liberally with salt and pepper and place it on top of the onions. Roast, uncovered, 20 minutes.
Step 3Remove the meat to a plate and stir the onions to keep them from sticking. Turn the meat over and place it back on top of the onions. Roast another 20 minutes uncovered.
Step 4Remove the meat to a plate again and stir the onions one more time. Replace the meat and add the red wine and the vinegar. Cover the meat loosely with a sheet of aluminum foil and then cover with a tight-fitting lid. Roast until the meat is falling-apart tender, about 1 1/2 to 2 hours more. Be sure to check the meat every 20 minutes, moving it around from side to side and stirring the onions underneath. For the last half hour, check every 10 minutes, adding more red wine as necessary to maintain a thick sauce consistency. After the first hour or so, the meat may seem really tight and tough, but keep cooking; it will become quite tender.
Step 5When the meat is fork tender, remove it from the oven but leave it in the pan until you're ready to serve. When ready to serve, carefully transfer it to a warm platter and spoon the onion marmalade over the top.