If you have the time, soak the millet (to remove the phytic acid – if you don’t have time or if you forget, don’t sweat it). Preheat the oven to 375˚F.
In a medium saucepan, bring 3 cups water to a boil. Add 1 teaspoon sea salt and the millet. Bring to boil. Reduce heat to low simmer; cover and cook 15-20 minutes, or until the water is absorbed and millet is tender. Stir in the butter or ghee, along with ½ cup of the cheese. Season to taste with additional salt, if needed. Cover and keep warm.
While the millet cooks, start the filling. In a 12-inch (preferably cast iron) skillet, heat the olive oil over medium-high heat. Add the onions with a pinch of salt and pepper. Cook, stirring occasionally, until the onions are tender, about 5-6 minutes. Add the mushrooms and cook, stirring occasionally, until softened, about 4-5 minutes. Sprinkle in the garlic, thyme and red pepper flakes. Add the tomato paste. Stir 1 minute. Add the Swiss chard and a pinch of salt and pepper; cook, stirring occasionally, until the greens are wilted. Stir in the tomatoes, ½ cup water, the cannellini beans and a pinch of cinnamon. Bring to a boil and simmer 3-5 minutes, or until thickened. Taste and season with salt and pepper as needed.
Dollop the millet over the filling and spread it out in a smooth layer (it doesn’t have to be perfect!). Sprinkle on the remaining cheese. Bake 15 minutes, or until bubbling and lightly golden around the edges. Let cool 5 minutes. Spoon the mixture into wide bowls and garnish with freshly sliced or torn basil (if you’d like) and grated Parmigiano.