In a large, heavy pot, heat 2 tablespoons extra-virgin olive oil and 1 tablespoon butter over medium heat. Stir in 2 large onions chopped into 1-inch cubes, 3 tablespoons apple cider vinegar, 2 tablespoons sugar, 1 bay leaf and 1 tablespoon fresh thyme leaves. Cover and cook, stirring occasionally, until the onions are tender, about 15 minutes. Remove the lid, increase the heat to medium-high and continue cooking, stirring frequently, until golden-brown, 15 to 20 minutes. Season with salt and pepper and let cool to room temperature.