Preparation

Make the soup

• Bring a large pot of well-salted water to a boil, and cook the pasta according to package directions until not quite al dente.
• Meanwhile, heat the oil in a 5- to 6-quart Dutch oven or other heavy-duty pot over medium heat until shimmering. Add the onion and 1/4 tsp. salt; cook, stirring occasionally, until starting to brown, 3 to 5 minutes. Add the squash and stir to coat with the oil. Add the parsley, sage, garlic, and pepper flakes, if using, and cook, stirring, until fragrant, about 30 seconds.
• Add the tomato paste and cook, stirring, until it is evenly distributed and looks slightly darker, 1 to 2 minutes. Add the wine and cook until almost evaporated, about 1 minute. Add the broth, beans, and tomatoes. Stir well, scraping the bottom of the pot, and simmer until the squash is barely tender, 13 to 15 minutes. Add the pasta and continue simmering until the squash and pasta are tender, 1 to 2 minutes. Remove from the heat.

Make the pesto and serve

• Put the parsley, sage, garlic, and coarsely grated cheese in a food processor. Sprinkle with 1/4 tsp. salt and 1/4 tsp. pepper and drizzle with the oil. Pulse until finely chopped, adding more oil if necessary to give it a saucy consistency. Season to taste with salt and pepper, and transfer to a bowl.
• Thin the soup with water if desired and add 1/4 tsp. pepper. Season to taste with more salt and pepper. Divide among soup bowls and spoon 1 to 2 Tbs. pesto on top of each serving. Pass the finely grated cheese at the table.