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Using a large, heavy, oven-proof skillet (I think enameled cast iron is perfect here), heat the ghee over medium heat. When it is melted and shimmering, add the onions with a pinch of salt.
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While they cook, preheat the oven to 375 F.
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Cook the onions, stirring occasionally, until they are caramelizing, about 10-15 minutes. You can add a splash of water if they start to scorch or stick. Add the garlic and cook for another 1-2 minutes, stirring.
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Add the finely chopped tender cilantro stems with another pinch of salt. Cook, stirring, for another 2 minutes.
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Add the turmeric and paprika and cook, stirring, for 30 seconds. Then add the cumin, coriander and garam masala and stir, cooking, for another 30 seconds.
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Add the tomatoes with all of their juices, as well as a pinch of salt and the bay leaves. Raise the heat to bring to a boil, and when it does boil, reduce the heat to maintain a simmer. Simmer for 20 minutes. Stir occasionally, being certain to scrape at the bottom of the pan.
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The tomatoes will reduce and thicken, and become more of a sauce. The oil will rise to the top of the sauce, kind of splitting from the sauce (it might look broken, but that is what you want).
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Dollop the yogurt into the sauce in several spoonfuls. Then lightly marble the yogurt into the tomatoes (this is O'Brady's technique and I thought it was brilliant).
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Use the wooden end of a spoon to create "holes" and crack each egg into a hole. Sprinkle with a little salt and black pepper, to taste.
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Bake in the oven to your preferred doneness; O'Brady recommends 12 minutes for oozing yolks but set whites.
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Sprinkle very lightly (the barest pinch) with garam masala when it comes out of the oven, and a handful of the chopped cilantro leaves. We enjoyed it with Basmati rice; if I had had any of them on hand, I am sure the garnishes listed above would also be delicious.