Coat a large stock pot with olive oil and add the onions, celery and carrots. Season with salt, to taste, and bring the pot to medium-high heat. Cook the vegetables until they start to soften and are very aromatic, about 10 minutes. Add in the garlic, crushed red pepper and thyme and cook for another 2 to 3 minutes. Add the chicken and fill the pot with enough water to cover the chicken. Add the bay leaves, bring the ingredients to a boil, then reduce the heat to a simmer. Cook for 30 minutes and skim off any particles that accumulate on the surface. Squeeze the juice of the 2 lemon halves into the soup and drop in the lemon halves. Add the cinnamon and nutmeg and taste for seasoning. Adjust the flavors with salt and pepper, if needed. Simmer the soup for an additional hour.
While the soup is simmering, bring another pot of well-salted water to a boil over high heat. Add the pasta and cook until "al dente," firm but not crunchy. Drain the pasta and transfer to a medium bowl. Add 1 teaspoon of olive oil and toss. Reserve.
After the soup has finished, switch the heat off and remove the chicken to a cutting board. Discard the lemon halves, thyme and bay leaves. Let the chicken cool, then remove the bones and discard. Pull the meat into bite-sized pieces and return them to the pot. Taste the soup for seasoning, which should be spicy with a bright lemon flavor and a warm cinnamon chicken feel. It should be very full-flavored and warm your soul. Rinse the beans and add them to the pot. Adjust the seasoning, if needed.
Spoon some of the reserved pasta into the bottom of each serving bowl and ladle the hot soup over the pasta. Garnish with the chopped cilantro and serve. This soup is perfect for a cold day! YAY!