In a glass bowl, combine the prunes and water. Cover with plastic wrap and microwave at high power for 2 minutes, or until the prunes are plumped. Let cool.
In a medium saucepan, heat the oil until shimmering. Add the onion and cook over moderately high heat until softened, about 5 minutes. Add the tomato and cook until slightly softened, about 4 minutes. Add the mustard seeds, cinnamon, nutmeg and crushed red pepper and cook until fragrant, about 1 minute. Stir in the prunes and their liquid, the vinegar, brown sugar and salt and simmer over moderately low heat, stirring occasionally, until jamlike, about 20 minutes.