In a small Dutch oven over medium-high heat, add the oil. When hot, add the onions and jalapeno and saute until just starting to caramelize, 4 to 5 minutes. Add the garlic and cook 1 minute more.
Reduce the heat to medium, sprinkle the onion mixture with the flour and stir constantly until lightly browned, about 2 minutes. Add the reserved liquid from the chiles, 1 cup water, the vinegar and salt and stir until the liquid is smooth and all the flour is dissolved.
Add the chiles and pepper and simmer for 5 to 6 minutes. Puree in a blender, or with a stick blender, and add the lime juice. Adjust to taste for salt and pepper. Refrigerate for up to 1 week.
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