Preheat oven to 400 degrees Fahrenheit. Wash and dice/chop squash, shallots and apples, making sure to keep squash separate from the others. Place squash on a parchment lined cookie sheet, sprinkle with salt and roast for 15 minutes. At the 15 minute mark, add apples and shallots to the cookie sheet. Roast another 30 minutes. Set aside to cool. Once cool, put in a food processor with the thyme and pulse until chunky. Do not puree into a mush or paste. Add to a large bowl.