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Preheat oven to 325 degrees.
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Spray a 1 quart baking dish with cooking spray. Set aside.
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In a large skillet over medium/high heat, cook the cut bacon until almost crisp.
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Use a slotted spoon to remove 3 tablespoons of the bacon to a plated lined with a paper towel. Set aside.
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Remove all but 3 tablespoons of the bacon grease from the skillet.
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Add the sliced onions, salt, pepper and garlic to the skillet with the remaining bacon, and cook, stirring occasionally, until the onions start to turn golden brown (approximately 10-15 minutes).
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Reduce the heat to low and stir in the maple syrup and the all purpose flour.
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Cook for an additional 1-2 minutes, stirring frequently.
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Turn off the heat and stir in the shredded cheeses. Stir well to combine.
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Spoon the dip into the prepared baking dish and top with the reserved partially cooked bacon and the fresh thyme leaves.
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Bake in the preheated oven for 15-20 minutes.
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Serve immediately with crackers, veggies, bread, or chips.
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Enjoy!