To make the ketchup: Place a rack about 4 inches from the broiler element and preheat. Arrange the tomatoes on a foil-lined baking sheet. Broil the tomatoes, turning occasionally, until blackened all over. Set aside to cool slightly. Core and roughly chop the tomatoes with their skins.
Heat the 2 tablespoons olive oil in a medium saucepan over medium heat. Add the onions and cook, stirring occasionally, until golden brown, about 10 minutes. Add the garlic, chipotles, cinnamon, allspice, and clove and cook, stirring, until fragrant, about 2 minutes. Add the vinegar and brown sugar and cook, stirring, until the liquid is slightly syrupy. Add the chopped tomatoes and salt and season with pepper, to taste. Reduce the heat to medium-low and cook, stirring occasionally, until thickened, about 15 minutes.
Pass the ketchup through a food mill, discard the seeds and skins. Return the ketchup to the saucepan and place over medium heat. Simmer, stirring occasionally to prevent scorching, until very thick, about 15 minutes. Store in the refrigerator at least 3 hours or overnight for the flavors to come together.
To make the potato skins: Place a rack in the middle of the oven and preheat to 375 degrees F. Pierce the potatoes all over with a fork. Bake the potatoes on the rack until tender, about 55 minutes. Set the potatoes aside to cool, about 30 minutes.
Meanwhile, put the garlic cloves and olive oil in a small saucepan and place over medium heat. Cook until the garlic sizzles, about 2 minutes. Reduce the heat and cook until the garlic is tender, about 10 minutes. Set aside to cool. Remove the garlic and reserve.
Raise the oven to 500 degrees F. Halve the potatoes lengthwise and gently scoop out the flesh, leaving about 1/4 inch of the flesh intact. Reserve the potato flesh for other recipes (See Cook's Note.)
Cut the potato halves in half lengthwise and transfer them to a baking sheet. Pour the garlic oil over the potato skins and turn them until completely coated. Arrange the potato skins skin-side down and bake until crispy, turning once, about 15 minutes.
Season skins with salt, to taste. Transfer the skins to a serving platter and serve with the ketchup. For an extra garlicky punch, chop up the reserved garlic and sprinkle it over the skins.
Cook's Note: Don't throw away that leftover potato flesh! Use it as thickener for soups or stews, make crispy potato cakes, or whip up a batch of impromptu croquettes.
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