Combine the apples, cranberries, raisins, brown sugar, orange juice, apple cider vinegar, salt, cinnamon, ginger, cloves, and red pepper flakes in a large saucepan.
Bring to a boil over high heat and reduce to simmer for about 25 minutes, until the apples have softened, the cranberries have burst, and the sauce has thickened.
Remove from the heat and transfer to an airtight container. Let cool and store in the refrigerator until ready to serve.
Notes
The original recipe I shared here called for 1/2 cup of apple cider vinegar without the orange juice. Over time, I've found that we prefer our chutney to be a little sweeter with less tang from the vinegar. If you prefer the original, skip the orange juice above and increase the vinegar to 1/2 cup.