Place the millet and amaranth in a pot with the vegetable stock. Bring to a boil, then reduce the heat to low setting and cover. Simmer until the liquid has been absorbed, about 30 minutes. Remove from the heat and set aside.
Preheat your oven to 350°F and have a 9 x 13-inch casserole dish ready.
While the grains are cooking, heat the oil in a large pan over medium-high heat. Sauté the onion until it becomes translucent and begins to brown, about 5 minutes. Add the garlic, mushrooms, carrots, and beans, and continue to cook, stirring frequenly, for about 10 more minutes, until the vegetables have softened.. Add the chard and kale, and cook until they become tender and bright green. You may need to add the greens in batches, depending on the size of your pan.
Transfer vegetables to your casserole dish. Carefully, spread the millet-amaranth mixture over the top. Cook in the oven for 30 minutes, until the crust is golden brown.