Cooking onions and mushrooms slowly for a long time concentrates their flavor, which adds depth without a ton of oil. Pairing the onion mixture with whole wheat pasta isn’t just a healthful whole grain choice either — the nutty flavor and sturdy chew of the noodles enhance the entire dish.
Heat 1 tablespoon olive oil in a large Dutch oven or wide pot over medium-high heat. Add the mushrooms and cook, undisturbed, until they are lightly browned and they start to soften, about 5 minutes. Stir well, then add the onions, paprika, remaining 2 tablespoons olive oil, 3/4 teaspoon salt and a few grinds of pepper. Cook, stirring occasionally (more frequently toward the end), until the onions are golden and very tender, about 30 minutes, reducing the heat to medium during the last 10 minutes so the onions don’t burn.
Meanwhile, bring a large pot of well-salted water to a boil. Add the pasta and cook as the label directs for al dente. Reserve 1 1/2 cups cooking water, then drain. Add the pasta, 3/4 cup cooking water, the sour cream and vinegar to the mushroom-onion mixture. Toss until the pasta is well coated and slightly saucy, gradually adding the remaining cooking water as needed.
Add about half each of the parsley, dill and chives to the pasta and toss; season with salt and pepper. Divide among bowls and top with the remaining parsley, dill and chives.