Pre-heat your oven to 350°F (177°C). Heat oil in a saucepan over medium heat. Add half of both the onion and garlic paste. Stir in thyme, pepper and hot pepper flakes (if using). Sauté for 5 min. or until onion is translucent. Stir in tomatoes, simmer for 15 min. until thickened. Stir in basil and cool sauce to room temperature.
Meanwhile, cook manicotti until still firm in the centre, 6 to 8 min. Place on a paper towel-lined baking sheet to cool. In the same water, cook rapini for 2 min. Cool under running water, squeeze dry and chop finely.
In a non-stick skillet on medium-high heat, combine chicken with remaining onion and garlic paste. Cook, breaking apart with a spoon, until chicken is browned. Transfer to a bowl and cool slightly. Add rapini, cottage cheese, 1/2 cup (125 mL) tomato sauce and 1/4 cup (60 mL) shredded cheese.
Spread 1 cup (250 mL) of sauce on the bottom of an 11 x 9-in. (2.5 L) baking dish. Fill manicotti shells with chicken mixture. Pour remaining sauce over manicotti and sprinkle with remaining cheese. Cover pan with foil and bake for 30 min. Then uncover and bake for 15 min. until bubbly and golden.
This warm and comforting recipe can be made ahead and reheated in minutes.