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Heat oven to 200C/180C fan/gas 6. In a roasting tin, toss the squash with 1 tbsp olive oil, salt, pepper and the thyme leaves. Cover the tin with foil and roast for 30 mins until the squash is tender.
Heat the remaining olive oil with the butter until the butter has melted and is foaming slightly. Throw in the sage leaves and cook for a couple of mins until crisp, then add the onion, garlic, chilli flakes and lemon zest. Cook, stirring, for about 8 mins, until the onion is soft and fragrant, add a drizzle more oil if needed. Mix in the breadcrumbs, toasting in the fat for a few mins.
Whisk the milk, eggs and cream together before adding the cheese. Remove the squash from the oven and turn the oven down to 170C/150C fan/gas 3. Combine the crumb mix with milk, eggs and cream. Pour over the squash. Scatter over the pumpkin seeds, then roast for another 15 mins. Remove from the oven and allow to settle for a couple of mins before serving.