1. Make caramelized onions: Put onions in a large frying pan with 1/2 cup water, cover, and bring to a boil. Reduce heat to low and cook, covered, until softened, about 30 minutes. Remove cover and cook, stirring occasionally, until liquid has evaporated and onions are golden. Increase heat to medium-high, add olive oil, and cook, stirring, until deep golden. Meanwhile, soak raisins in hot water 15 minutes; drain.
2. Stir in spices and honey; then stir in raisins and cook, stirring, until nutty brown, about 5 minutes. Set aside.
3. Make couscous and vegetables: Halve carrots and zucchini; cut into 1 1/2-in. pieces. Halve jalapeño (seed it if you want less heat). Peel and quarter turnips. Peel and seed squash; cut into 1-in. chunks.
4. Heat olive oil in a large pot over medium heat. Add 1 tsp. salt, the pepper, saffron, cumin, and cinnamon sticks and fry, stirring, 1 minute. Add vegetable stock and bring to a boil. Add carrots, turnips, and jalapeño and simmer, covered, 15 minutes. Add squash and zucchini and cook, covered, until all vegetables are soft but not falling apart, about 20 minutes.
5. Transfer 2 cups hot stock from vegetable pot to a 4-qt. saucepan. Add 1 cup water and remaining 1/2 tsp. salt. Bring to a boil, stir in couscous, and cook, covered, until tender, 6 to 8 minutes.
6. Transfer 2 cups stock from vegetable pot to a pitcher and stir in harissa to taste.
7. Spread couscous on a platter, making a well in the center. Using a slotted spoon, arrange vegetables, including cinnamon sticks, in the well; discard jalapeño. Scatter onions on top and sprinkle with cilantro. Moisten the couscous with some stock and strain the rest into a second pitcher. Serve couscous and vegetables with the two stocks (plain and spicy) on the side.
*Buying cubed butternut squash will save you some time. Harissa's heat level varies wildly depending on the brand, so taste before adding.
Make ahead: Up to 1 day. Finish making all five components of the dish—caramelized onions, vegetables, couscous, harissa-spiked stock, and plain stock—and chill separately. Ten minutes before serving, reheat in a microwave and serve as directed.
Note: Nutritional analysis is per serving.