Heat the oil in a large, deep skillet over medium-low heat. Add the onions, 1 teaspoon of the salt, cumin, and cinnamon. Cook until the onion is softened, about 10 minutes, stirring frequently.
Raise the heat under the skillet to medium high and add the chiles. Cook for about 5 minutes, stirring frequently. Add the garlic and cook for one minute. Add the chile powder and cook an additional minute. Reduce the heat back to medium-low, cover the skillet, and cook for about 5 minutes, stirring occasionally. Add the warm water (I heated mine in the microwave for 2 minutes), cover and cook another 15 minutes.
Stir in the squash, the remaining teaspoon of salt, and the lime juice. Adjust the the heat to low, cover the skillet, and cook for 15 minutes more You want the squash to be just tender, but not mushy.
Gently stir in the beans, cover, and cook for only about 5 more minutes. Taste to see if more lime juice is needed.
Serve hot, offering the toppings of sour cream (or yogurt), toasted pepitas, and minced cilantro or parley, if desired.