Step 1Heat a large heavy-bottomed pot over high heat for 2 minutes. Add the olive oil, rosemary and chile. When the rosemary and chile start to sizzle, add the onion, fennel, carrot, celery, garlic, thyme, parsley, bay leaf, fennel seeds, peppercorns and salt.
Step 2Saute the vegetables for 8 to 10 minutes, stirring often, until they begin to caramelize. Add the tomatoes and cook for 5 minutes.
Step 3Add the water, bring to a boil and simmer until the vegetables are soft, about 10 minutes. Cool slightly, then puree in a blender, in batches if necessary. Strain. Cool completely.
Step 1Pound the garlic in a mortar with the salt until it forms a paste. Place in a small mixing bowl. In batches, pound the basil to a paste, transferring the paste to the bowl as you go.
Step 2Stir the olive oil into the basil. When the basil has all been incorporated, pound the parsley in the same manner and add to the bowl. Gently pound the pine nuts and add to the bowl. Stir; taste for seasoning.
Step 1Heat the oven to 350 degrees. Heat a medium saute pan over high heat for 1 minute. Add 2 tablespoons olive oil and the onion. Cook until the onion is translucent. Add the fennel, thyme leaves, salt and pepper. Cook until the fennel is tender, 1 to 2 minutes. Remove to a plate to cool.
Step 2Return the pan to the stove, add 2 tablespoons olive oil and quickly saute the squash over high heat for 1 or 2 minutes. Remove to a plate to cool. Blanch the cut beans for 2 minutes in boiling salted water. Cool in an ice bath. When the vegetables have cooled, add them to the soup. Add the shell beans; taste for seasoning.
Step 3Cut the crust from the bread and tear the remaining bread into rustic 1-inch pieces. Using your hands, toss with the remaining 2 tablespoons olive oil and the Parmesan, squeezing the bread gently to help it absorb the oil. Arrange the croutons in a single layer on a baking sheet and toast, stirring often, 12 to 15 minutes until golden brown and crisp outside but a little tender inside.
Step 4Heat the soup to boiling. Stir in the amaranth. Ladle the soup into bowls and garnish each with a spoonful of pistou and a handful of croutons.