Heat a large pot over medium heat and add olive oil and butter. Add onions with pepper flakes and a pinch of salt and stir to coat, then cook until softened, about 5 minutes. Add in garlic and cook for another minute. Stir in the pepper flakes, squash cubes, salt, pepper, paprika and nutmeg. Stir to coat the squash. Cover the pot and cook until the squash has softened slightly, about 6 to 8 minutes, stirring occasionally. Pour the stock into the pot and bring the mixture to a simmer. Cook until the squash is completely tender.