Preheat the oven to 375°F.
Place the squash on a baking sheet and roast for 40 minutes, or until you can easily pierce the narrow end with a fork. Allow the squash to cool until you can comfortably handle it. Remove the skin, halve lengthwise, remove the seeds and fibers, and dice. Set aside.
Heat 1 tablespoon of water in a large pot over medium heat. Add onion, celery, and garlic and sauté until the onion is translucent and begins to turn golden. Add more water to keep the vegetables from burning, about 1 tablespoon at a time.
Add the sweet potatoes, pumpkin, and broth to the pot and bring to a low boil. Add the bay leaves, cumin, fennel seeds, crushed red pepper, and cloves, and reduce to a simmer. Cover the pot and cook for 10 minutes.
Stir in the roasted squash and simmer over low heat until all the vegetables are tender about 15 minutes. Use a slotted spoon to scoop out 2 cups of the vegetables and transfer to a medium bowl. Using a fork mash the vegetables well, return them to the pot, and stir to combine. Alternatively, you could use an immersion blender or transfer the mixture to a blender and blend the soup until completely smooth. Taste the soup and adjust the seasoning with vinegar and garnish with pepitas, if desired.
