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Preheat the oven to 400 degrees Fahrenheit and line a large, rimmed baking sheet with parchment paper for easy clean-up.
To prepare the squash, use a sharp chef’s knife to slice through it from the tip to the stem. I find it easiest to pierce the squash in the center along a depression line, then cut through the tip, and finish by slicing through the top portion just next to the stem. Use a large spoon to scoop out the seeds and stringy bits inside, and discard those pieces.
Place the squash halves cut side up on the parchment-lined pan. Drizzle 1 tablespoon of the olive oil over the squash, and sprinkle with 1/4 teaspoon of the salt. Rub the oil into the cut sides of the squash, then turn them over so the cut sides are against the pan. Bake until the squash flesh is easily pierced through by a fork, about 30 to 45 minutes. Leave the oven on.
Meanwhile, cook the quinoa: In a medium saucepan, combine the rinsed quinoa and water. Bring the mixture to a boil over medium-high heat, then reduce the heat as necessary to maintain a gentle simmer. Simmer, uncovered, until all of the water is absorbed, 12 to 18 minutes. Remove the pot from the heat and stir in the cranberries. Cover, and let the mixture steam for 5 minutes. Uncover and fluff the quinoa with a fork.
In a medium skillet, toast the pepitas over medium heat, stirring frequently, until the pepitas are turning golden on the edges and making little popping noises, about 4 to 5 minutes. Set aside.
Pour the fluffed quinoa mixture into a medium mixing bowl. Add the toasted pepitas, chopped green onion, parsley, garlic, lemon juice, the remaining 1/4 teaspoon salt, and the remaining 1 tablespoon olive oil. Stir until the ingredients are evenly distributed. Taste and add additional salt, if necessary.
If the mixture is very hot, let it cool for a few minutes before adding the Parmesan cheese and goat cheese. Gently stir the mixture to combine.
Turn the cooked squash halves over so the cut sides are facing up. Divide the mixture evenly between the squash halves with a large spoon. Return the squash to the oven and bake for 15 to 18 minutes, until the cheesy quinoa is turning golden on top.
Sprinkle the stuffed squash with the remaining 1 tablespoon chopped parsley, and serve warm.