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.
Stir in spices and honey; then stir in raisins and cook, stirring, until nutty brown, about 5 minutes. Set aside.
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.
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.
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.
Transfer 2 cups stock from vegetable pot to a pitcher and stir in harissa to taste.
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.