Pre-heat your oven to 180′ C. Rub the onions (skin on) with olive oil and fit snugly into a baking dish. Drizzle with the balsamic vinegar reduction. Sprinkle with the sugar, fresh thyme, a few grinds of black pepper and a pinch of sea salt. Bake for 90 minutes, basting halfway through. You want the balsamic vinegar to become sticky and glossy, but make sure it does not burn. If it starts going too dark, turn the heat down a notch or cover the dish with foil. The onions are ready when they are completely soft on the inside. Prepare the garlic croutons by removing the crusts from the bread. Slice into fingers and rub with the garlic. Drizzle with olive oil. Place in the oven with the onions and bake until golden (about 12 minutes). Remove and set aside. When the onions are done, cut a cross section into the tops and stuff with pieces of garlic crouton and chunks of cheese. Sprinkle liberally with more fresh thyme. Pop into the oven until the cheese has melted.
Photograph: Dirk Pieters