Preheat oven to 350 degrees F. Line an 8-inch springform pan with parchment paper, allowing the parchment to extend about 1 inch above the edge of the pan. Wrap foil tightly around the outside of the pan to prevent any leaking. Set inside a shallow baking pan. Set pans aside.
In a 12-inch skillet heat 1 tablespoon schmaltz over medium heat. Add rutabaga; season with salt and pepper and nutmeg. Cook and stir for 7 minutes. Add squash and sweet potato; cook for 10 minutes more or until vegetables are tender, stirring frequently. Remove from skillet. Add remaining fat to skillet. Add onion. Cook and stir for 4 to 5 minutes or until tender; add chard leaves and cook until tender (4 to 5 minutes). Remove from skillet to a colander set over a bowl. Press out liquid. If desired, add chard stems to skillet. Cook and stir for 5 minutes or until tender.
In a large bowl whisk together the eggs, oil, parsley, crackers, and 1/2 teaspoon salt until well-combined.
Place the chard mixture in the bottom of the prepared pan. Top with half of the rutabaga mixture, then prunes. Top with remaining rutabaga mixture. Carefully pour the egg mixture over layers. Sprinkle with chard stems, if using. Bake for 1 1/4 hours or until set in the center (160 degrees F). Remove and cool in pan for 15 minutes. Remove foil and sides of pan. Peel away parchment paper. Serve warm or at room temperature.