For the chickpeas: In a large pot, combine the soaked chickpeas, onion, carrot, celery, garlic, bay leaves, and thyme bundle. Fill the pot with water to cover the beans by 2 inches. Bring the water to a boil, reduce to a simmer (BTB, RTS), and cook for about 1 hour. Do the 5-bean test: Bite into 5 beans; if they are all properly cooked, carry on. If not, cook the beans for another 10 to 15 minutes and try again. Remember, beans cook at different rates, so you need to check a few to make sure they're really done!
When the beans are cooked, turn off the heat and season the water generously with salt. TASTE the water to be sure it is adequately seasoned. Let the beans sit in the salty water for 15 to 20 minutes to absorb some of the salty flavor. Remove the onion, carrot, celery, garlic, bay leaves, and thyme bundle and discard. Reserve 1 cup of the cooking water, strain the beans, and set aside.
For the stew: You can start this part while the beans are cooking: Coat a large wide pot with olive oil, toss in the onions, and season with salt and the crushed red pepper. Bring the pan to medium heat and cook until the onions are soft and very aromatic, 8 to 10 minutes. Add the garlic and cook for another 1 to 2 minutes.
Toss in the diced squash, cumin, fennel, tomatoes, and the reserved bean water (if you forgot to save the bean water, tap water is fine). Stir to combine, taste, and season with salt if needed. Bring the mixture to a boil and reduce to a simmer (BTB, RTS). Cook for 25 to 30 minutes or until the squash is cooked through. Add another cup of water if the liquid has evaporated too much.
Toss in the reserved chickpeas and cook for 15 to 20 minutes or until the mixture is thick and stewlike. Serve hot or at room temp, garnished with chives.