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Preheat the oven to 375°F. On a rimmed baking sheet, toss the cauliflower and butternut squash with 1 tablespoon of the oil, 1/2 teaspoon salt, and a few grindings of pepper. Roast the vegetables for 15 minutes, lower the heat to 350°F, and roast 15 minutes longer.
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Meanwhile, in a large skillet over medium heat, warm 1-1/2 teaspoons oil until hot but not smoking. Add half of the shallots and sauté, stirring occasionally, until they start to soften and brown, 3 to 5 minutes. Add the garlic and stir until just toasted, 1 to 2 minutes. Transfer the mixture to a blender, add the roasted cauliflower and butternut squash, the vegetable broth, liquid aminos, and 3/4 teaspoon salt, and blend until smooth. Cover and set aside.
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In a food processor, combine the whole almonds, 5 teaspoons oil, 1/4 teaspoon salt, a few grindings of pepper, and the nutmeg. Pulse just until the topping is crumbly (if you process too long, you’ll get almond butter or dust). Add the rice cereal and pulse until crumbly. Set aside.
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In a large skillet over medium heat, add 1 tablespoon oil, the remaining shallots, the celery, and carrots. Sauté, stirring occasionally, until softened and beginning to caramelize, about 7 minutes. Add the mushrooms and sauté, stirring occasionally, for 5 minutes. Add the thyme and parsley and cook, stirring occasionally, for 2 minutes. Add the chickpeas, cooked wild rice, reserved cauliflower mixture, and 1/2 teaspoon salt. Stir for 1 minute, then turn off the heat. Season to taste with salt and pepper and add the lemon juice. Transfer to a 9- to 10-inch casserole dish.
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Evenly distribute the almond topping, sprinkle the slivered almonds over the casserole, and bake, uncovered, until bubbling, 25 to 35 minutes. For extra browning, broil 1 to 3 minutes. Let rest for 10 minutes, garnish with thyme and parsley, and serve.