Combine the onion, ginger, orange juice, vinegar, brown sugar, mustard seeds, red pepper flakes, and salt in a medium-size saucepan. Add the apples, adding them as you chop to keep them from turning brown. Bring to a boil over medium-high heat, stirring occasionally. Reduce the heat and simmer for 50 minutes to 1 hour, stirring occasionally, until most of the liquid has evaporated. Stir in the raisins and serve warm, at room temperature, or cold.