Preheat oven to 350 degrees F.
Spread pecans in a single layer on a small baking sheet. Bake until golden and aromatic, 8 to 12 minutes. Shake the pan halfway through baking to make sure nuts toast evenly. Cool and coarsely chop; set aside.
Combine cranberries, apples, orange zest and juice, sugar, water, vinegar, onion, apricots, ginger, red pepper flakes, and nutmeg, in a large saucepan. Place over medium heat and cook, stirring frequently, for 30 minutes. Stir in pecans. Cool to room temperature, and serve, or store refrigerated in an airtight container for up to 1 week.
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