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Put the oil in a medium saucepan over a medium heat, add the flour and stir well. Still stirring, slowly pour in a little of the milk and mix well until smooth. Add a little more milk, repeating until all the milk has been added and you have a smooth sauce. Stir in the nutmeg, season, then take off the heat while you cook the pasta.
Heat oven to 220C/200C fan/gas 7. Bring a large pan of water to the boil, add the macaroni and boil for 8 mins. Add the runner beans and green beans, and boil for a further 3 mins.
Drain the pasta and the beans, and tip into a large gratin dish. Pour over the prepared sauce and tuck the chopped cheese in among the pasta, then top with the grated cheese and pumpkin seeds. Bake for 10-15 mins or until the top is bubbling and golden. Serve with a peppery salad, if you like.