Roasted Root Vegetables: Preheat oven to 425°F. Toss together root vegetables, thyme, rosemary, oil, garlic, salt and pepper. Arrange in single layer on parchment paper–lined baking sheet.
Roast vegetables for 30 to 35 minutes or until golden brown and tender; let cool completely. Add to food processor; pulse until coarsely chopped into smaller chunks.
Cream Sauce: Meanwhile, melt butter in saucepan set over medium heat; cook onion and thyme, stirring, for about 5 minutes or until softened and lightly golden.
Sprinkle flour over top; cook stirring, for about 1 minute or until smooth. Slowly whisk in milk until smooth; bring to boil, whisking constantly. Reduce heat to medium-low; cook, stirring frequently, for 12 to 15 minutes or until sauce thickens slightly. Season with pepper and nutmeg. Remove from heat. Stir in ricotta and Parmesan cheese; set aside.
Manicotti: Meanwhile, reduce oven heat to 375°F. In large pot of boiling water, cook pasta according to package directions. Drain and let cool completely.
Spread half of the sauce in bottom of greased 8-inch square baking dish. Stir ricotta, egg yolk, mozzarella and 1 tbsp chives into vegetable mixture. Spoon filling into piping bag fitted with large round tip; pipe into each end of manicotti shell to fill. Arrange manicotti in prepared pan; pour remaining sauce over top.
Cover with foil and bake for 30 minutes. Remove foil; bake for about 15 minutes or until filling is heated through. Sprinkle with walnuts and remaining chives.
Use roasted root vegetable filling to stuff large shells or cannelloni if desired.
For nut-free manicotti, substitute toasted pumpkin seeds for walnuts.