Preheat oven to 350°F and toss the first 7 ingredients in a bowl. Spread mixture on a parchment-lined pan and bake until the vegetables are lightly browned and soft when pierced with a knife (about 40 minutes). Cool for about 10 minutes. Transfer cooked mixture to the bowl of a food processor and blend well. Add flour and cheese and blend again. With the mixer running, add the eggs. Season to taste. Place mixture in a piping bag fitted with a round tip and pipe into manicotti shells. Place in a lightly greased casserole dish and bake for about 20 minutes (or until the filling is set and the noodles are completely cooked). Serve with your favourite pasta sauce. (We used a white wine cream sauce.)