Begin by making the pastry. Place the flour and butter in a food processor and process until the mixture resembles bread crumbs. Add the egg yolk and water and pulse until the mixture begins to come together to form a ball. Remove from the food processor and place onto plastic wrap and shape into a disc. Refrigerate for 30 minutes.
Remove the pastry from the refrigerator and roll out the pastry on a lightly floured bench or silicone baking mat until approximately 5mm thick. Cut out 4 circles of roughly 20cm (8 inches) in diameter and place onto a baking tray lined with baking paper. Refrigerate until needed.
Preheat the oven to 180 celsius (350 fahrenheit) and toss the butternut pumpkin with the olive oil and season with salt and pepper. Place in a roasting pan lined with baking paper and roast for 25 minutes or until tender. Leave to cool slightly.
Remove the pastry from the refrigerator and place a spoonful of the caramelised onion relish in the center of the pastry circle and use a spoon or knife to spread it evenly leaving a border of roughly 5cm (2 inches). Place the pumpkin on top of the caramelised onion mixture and season with sea salt. Bring up the pastry border, to enclose the filling, pleating as you go. Finally rub the thyme leaves between your fingers to release their scent and sprinkle over the top of the crostata. Bake for 20 to 25 minutes, or until the pastry is lightly golden. Serve immediately.