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.
The chutney can be refrigerated for up to 2 weeks.