Heat a medium saucepan, lightly coated with olive oil, over medium heat. Add the onions and cook until the onions are lightly browned (about 5 minutes).
Add the garlic and continue cooking until the garlic has softened (about 2 minutes).
Add red chili flakes, brown sugar, vinegar, wine, mustard seeds, and raisins. Decrease the heat to medium-low. Cook the chutney until the liquid has evaporated and the onions are very soft (about 20-30 minutes).