Warm 1 tablespoon of olive oil in a large soup pot over medium-low heat. Sauté your onion, celery and carrots until onion is translucent, about 5 minutes. Add garlic and sauté, stirring, for another minute, until fragrant. Add all the spices, except the chili flakes, and cook for another minute, stirring frequently as not to burn.
Stir in the crushed tomatoes, and then add the lentils, water, and broth. Stir it all well and bring to a boil. Lower heat, cover and simmer on low until lentils are cooked through, about 45 minutes.
Meanwhile, heat your oven to 400 and spread your cubed butternut squash onto a lined baking sheet. Toss with 2 tablespoons of olive oil, chili flakes, sea salt & pepper. Roast for 30-40 minutes, a few times to make sure nothing is burning.
Stir beans into the chili pot and let heat through for about 5 minutes then, gently stir in the roasted squash. Add sea salt and pepper to taste.
Garnish with shredded cheese, sour cream, and green onions if desired.