Preheat the oven to 350°F (175°C). Line a muffin tin with paper liners or lightly grease it with oil.
In a large mixing bowl, combine the flour, oats, sugar, baking powder, baking soda, salt, cinnamon, and nutmeg (if using). Whisk until well combined.
In a separate bowl, mix together the applesauce, almond milk, vegetable oil, vanilla extract, and apple cider vinegar.
Pour the wet ingredients into the dry ingredients and stir until just combined. Be careful not to overmix.
Fold in the chopped apples, nuts, and raisins (if using).
Divide the batter evenly among the muffin cups, filling each about ⅔ full.
Bake in the preheated oven for 20-25 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Allow the muffins to cool in the tin for about 5 minutes, then transfer them to a wire rack to cool completely.