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Halve and thinly slice the onions, then thinly slice the garlic. Melt the butter with the oil in a large, heavy-based saucepan over a high heat. Tip in the onions and garlic and give them a good stir so they are glossed with butter. Sprinkle over the sugar, thyme leaves, chilli flakes if using and some salt and pepper. Give everything another really good stir and reduce the heat slightly. Cook uncovered for 40-50 minutes, stirring occasionally. The onions are ready when all their juices have evaporated, they’re really soft and sticky and smell of sugar caramelising. They should be so soft that they break when pressed against the side of the pan with a wooden spoon. Slow cooking is the secret of really soft and sticky onions, so don't rush this part.
Pour in the wine, vinegar and port and simmer everything, still uncovered, over a high heat for 25-30 minutes, stirring every so often until the onions are a deep mahogany colour and the liquid has reduced by about two-thirds. It’s done when drawing a spoon across the bottom of the pan clears a path that fills rapidly with syrupy juice. Leave the onions to cool in the pan, then scoop into sterilised jars and seal. Can be eaten straight away, but keeps in the fridge for up to 3 months.