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Tip the flour, salt and yeast into a bowl. Pour in the water, spoon in the oil and mix to a soft dough. Turn out on to a lightly floured surface and knead for 5 minutes until the dough is smooth and no longer sticky.
Return the dough to the bowl, cover with cling film or a damp tea towel and leave it to rise for 45 minutes to 1¼ hours or until the dough springs back when pressed. Don't worry too much is it takes more or less time – it's not critical for this relaxed recipe.
While the dough is rising, heat the oil in a large, deep frying pan or sauté pan, throw in the onions and fry gently for about 10 minutes until softened but not browned, stirring from time to time.
Sprinkle in the thyme and some salt and pepper, then tip in the tomatoes and stir well. Cover and cook gently for 45 minutes until the onions are meltingly soft, stirring occasionally and removing the lid for the last 10 minutes to reduce any liquid. Remove from the heat and leave to cool slightly.
Preheat the oven to 220C/gas 7/fan 200C. Lightly oil a shallow 23x33cm baking tin or tray. Knead the dough again briefly, then roll it out and press it into the tin. Don't leave it to rise again.
Spread the onion mixture over the dough, then arrange the anchovies on top, making a criss-cross pattern. Stud each window between the anchovies with an olive, then bake for 25-30 minutes until golden. Serve warm, cold or reheated, cut into squares.