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Cook bacon in a large, deep skillet over medium heat, stirring occasionally, adjuring the temperature so the bacon cooks evenly but the glaze in the bottom of the skillet does not burn, until the bacon is crisp and browned, about 10 minutes. Transfer bacon to paper towels to drain, leaving the fat in the skillet.
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Stir in the onions with 1 teaspoon salt and ½ teaspoon pepper. Cover the skillet and cook, stirring occasionally, until the onions are softened, about 5 minutes. Reduce the heat to medium-low. Cook uncovered, stirring occasionally, until the onions are very tender and golden brown, about 25 minutes.
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Stir in the reserved bacon with the vinegar, maple syrup, bourbon, and thyme and bring the t a simmer over medium heat. Return the heat to medium-low simmer, stirring often, until the liquids have reduced to a few tablespoons and the mixture is thick and spreadable, about 10 minutes. Transfer it to a bowl and let it cool (remove from refrigerator 1 hour before serving). Serve at room temperature.