Preheat your oven to 400 degrees and line a baking sheet with foil. Roughly chop your bell peppers and onion. Add butternut squash, and whole cloves of unpeeled garlic. Drizzle everything with ΒΌ cup of olive oil, then sprinkle with your salt, thyme, red pepper flakes and ground black pepper. Use your hands to toss everything well. Place in the oven and bake for 30-40 minutes or so, until the squash is tender. Remove your vegetables from the oven and pick out the garlic cloves. Squeeze the garlic out of its peels and add it to the vegetable mix. Puree the vegetables in Cuisinart in batches until smooth, then add to a large stockpot (or, add the vegetables directly to your stockpot and puree with an immersion blender. Add the broth and stir. Heat the soup over medium until warmed through. Taste and adjust seasonings as needed. Add yogurt right before serving and stir thoroughly. Divide your soup among your bowls add toasted half bagel, and sprinkle with goat cheese and fresh thyme if you have it. This soup will keep well in an airtight container in the refrigerator for up to 5 days, or frozen for up to 5 months.