Heat the extra-virgin olive oil in a saucepot over medium to medium-high heat. Add the onions, chiles and ginger to the pan and cook to soften, 10 to 12 minutes. Add the apples, dark brown sugar, thyme, maple syrup, cider vinegar, lemon juice, a little salt and nutmeg. Cover and cook, stirring occasionally, until a thick sauce forms, 15 to 20 minutes. Adjust the seasoning and transfer to a serving dish.