1For the garlic: Preheat oven to 350-degrees. Peel garlic and cut any large cloves in half so that all cloves are roughly the same size. Place in a small ramekin with 1/4 cup olive oil and a pinch of sea salt. Cover tightly with foil and bake for 20-40 minutes. Cooking time ranges significantly depending on the size of garlic cloves, so check them every 5 minutes or so after 20 minutes. Continue to bake until garlic just begins to brown on the edges. Remove from oven and let cool in oil, uncovered. I like to make the garlic while the soup is simmering and simply add the garlic when pureeing, but you could make garlic ahead of time to add to soup while simmering.
2For the soup: Use a vegetable peeler to carefully remove the skin. I trim off the neck of the squash first, then cut both the bulb and the neck in half. Cube the neck into small half-inch or slightly larger cubes and set aside. Use a sharp spoon to remove the stringy flesh and seed from the bulb halves. Slice bulbs into strips and then chop each strip into small wedges roughly the same size of the cubes. Set aside. If using a portion of sweet potatoes, peel and chop sweet potatoes into equally sized cubes.
3Heat 2 tablespoons of olive oil in a large soup pot over medium heat. Add sliced onions and sauté for 5 minutes or so. chop 2-3 tablespoons for fresh sage into small strips and add to the pot. Sauté for an additional minute or two, until sage is fragrant but not crisped. Add squash (and sweet potatoes, if using) to the pot along with the chili flakes, nutmeg, a half teaspoon of salt to start and a few cracks of fresh black pepper. Add just enough stock to semi-submerge the cubed veggies. Better to have not enough liquid than too much - you can always add stock later in the blending process.
4Cover pot and bring to a simmer, then lower heat and simmer until vegetables are extra tender. By this time your braised garlic should be finished. Add garlic drained from oil at any point to simmering soup.
5You could use an emersion blender or transfer batches of the soup to a blender to purée until smooth. Add additional broth until you reach desired consistency. Taste to adjust seasoning. Serve immediately, or return to soup pot to simmer if soup has cooled off considerably while blending.
6For the fried sage: I wouldn't make them ahead of time, as they will loose their crispness. Just make a few fried sage leaves per serving to top your bowls of soup.
7Transfer the oil used for braising the garlic to a small skillet or sauté pan. Heat over medium heat, being careful to keep oil under the smoke point. Trim a few sage leaves and add to preheated oil. (You can test one first, to make sure oil is hot enough - it should sizzle instantly) Watch closely, as they fry quickly. I wait until just the very tips start to turn slightly brown. Strain from oil and place onto a paper towel to drain. Leaves should be brittle yet still vibrant green.