While the onion is cooking, we snap off both ends of each green bean. Discarding the ends, we place the green beans on a plate. When all the green beans are trimmed, we add them to the pan, along with the garlic, and stir. Using a sharp knife, we cut each tomato, removing the skin and flesh, leaving the seed pod. We chop the tomatoes, yielding about ¾ cup, and add them to the pan. We add some salt and pepper and the water, then raise the heat to medium-high. When the mixture is boiling, we lower the heat to medium-low, cover, stir occasionally, and cook for 20 minutes.
After 20 minutes, the green beans are tender and the liquid has reduced to a nice glaze. We taste for salt and pepper and serve warm sprinkled with hot pepper flakes.