Combine salt, pepper, cumin, chili powder, oregano, paprika, garlic, and oil in a small bowl. Rub seasoning over the side of the beef without the fat cap and let sit for 20 minutes.
Place the brisket, fat side up, in a roasting pan. Add the beef stock and beer, cover, and braise in the oven for 3 ½ to 4 hours or until brisket can easily be shredded with a fork. Remove from oven. Skim fat from cooking liquid and reserve 1 cup.
Prepare the onion jam. Heat oil in a nonstick saute pan over medium heat. Add onions and cook until caramelized about 40 minutes. Add a little bit of water if the pan becomes too dry.
Add flour and stir to coat the onions. Add balsamic vinegar, brown sugar, thyme, and reserved cooking liquid. Bring to a boil, reduce heat to low, and simmer for 10 minutes. Season with salt and pepper. Serve with brisket.
Notes
You can caramelize the onions the day before and reheat them before finishing the jam.You can marinate the brisket overnight in the seasoning mix.