1. Bring cranberries, raisins, sugars, garam masala, ginger, orange zest, and orange juice to low boil, then simmer for 5 minutes uncovered. Add the apples, returning to a low boil, and simmer uncovered until apples are soft and liquid is thickened. Refrigerate overnight to bring out flavors. Leftover chutney can also be stored for several days in the refrigerator and used in other recipes.
2. Preheat oven to 400°F.
3. Unroll the refrigerated Flatbread Dough and using a 3 in. cutter or small cup, cut circles out of dough. Also cut the parchment paper so that it can be placed in the muffin tin molds if not using a nonstick muffin pan. Place each dough circle in the muffin molds on top of the parchment paper and create little cups. Prick the dough with fork tines and bake for 8 minutes. Remove from oven.
4. Cut small wedges of the cheese and place on top of the dough and bake for another 2 minutes until cheese is semi-melted. Spoon chutney mixture into cups. Serve warm.