Cut the onions in half, and then slice them into 1/8-inch-thick half-rounds. (You will have about 10 cups of onions.)
Heat the olive oil in a large saute pan over medium heat. Add the onions and saute for 15 to 20 minutes. Add the peppers, garlic, vinegar, tomato puree, pepper flakes, salt and pepper and continue cooking an additional 10 minutes.