In a big roasting pan combine everything, coat well with olive oil and roast in a preheated 400 degree F oven. Stir occasionally until everything is caramelized and black around the edges. Season with salt and pepper.
Run everything through a food mill on a medium dye over a medium pot.
If too thick, thin with water. Add milk right before service.
Cut whole-wheat bread into cubes and place into a large bowl, add chopped garlic and red pepper flakes. Season with salt and pepper and toss with olive oil. Transfer to a sheet pan and place in the oven for 5 to 7 minutes, until golden brown.
Mix 1 pint of Greek yogurt with chopped chives. Season with salt and pepper.
Garnish the soup with croutons and yogurt.