Preheat the oven to 400°F. Scatter the pecans on a small baking sheet and let them toast while the oven heats up, for about 6-7 minutes. Set a scant ¼ cup of the pecans aside for garnishing your soup and chop them up roughly. You'll be blending the remaining ½ cup with the soup.

Line a large baking sheet with parchment paper (or 2 medium).

Peel the squash and remove the seeds before dicing into 2-inch chunks. Place the diced squash on the parchment-lined baking sheet.

Peel and core the apples and then dice them into chunks as well. Add them to the baking sheet. Peel the onions and chop them roughly. Add them to the baking sheet.

Add the peeled garlic, sliced ginger, chili flakes, and olive oil to the baking sheet. Season generously with salt and pepper. Toss to coat everything evenly and then spread out into an even layer. Slide the tray into the oven.

Roast the squash, apples, and onions until soft and browning a bit on the edges, about 40-45 minutes. Remove and let cool slightly.

Transfer half of the roasted squash mixture to an upright blender. Add half of the toasted pecans to the blender and 2 cups of the vegetable stock. Blend this mixture on high until smooth, about 1-2 full minutes. Pour the blended soup into a large pot. Repeat this process with the remaining roasted squash, pecans, and stock.

Once you have all the blended soup in the pot, stir in the apple cider vinegar and Tamari. Give it a stir and check the seasoning. Adjust if necessary (more salt, vinegar, chili etc). Bring the soup to a boil over medium heat. If the soup is too thick for your liking, add some water to thin it out. Serve the soup hot with toasted pecans on top.