Preheat oven to 375 degrees. Spray two (24 each) mini muffin tins with cooking spray.
Put the pine nuts in a dry skillet and cook over medium heat, stirring frequently, until lightly browned, 3 – 4 minutes. Set aside.
In a large mixing bowl combine the focaccia mix, 4 tablespoons olive oil, 4 eggs, water, and 1 cup parmesan cheese. Dump the mixture out onto a clean work surface and knead until a smooth dough forms, about 1 – 2 minutes. Divide into 48 equal sized balls. Place the balls in the muffin tins and make an indentation with your thumb into each ball forming a cup.
Heat the remaining 2 tablespoons of olive oil in a large skillet over medium-high heat. Add the onion and cook, stirring often, until soft and translucent, about 5 minutes. Add the scallions and cook for 1 minute. Squeeze all the moisture from the spinach and add to the onions. Cook, stirring, until the spinach is totally dry. Put in a mixing bowl; add the reserved pine nuts, feta, ricotta, salt, pepper, and nutmeg. Stir to combine. Spoon the filling into the cups. Sprinkle the remaining ½ cup Parmesan on top of the cups and bake for 15 minutes or until lightly browned. Serve hot, warm, or at room temperature.