In a large bowl, combine milk, vinegar, and rolled oats. Let sit one hour to soften oats.
Preheat oven to 375°F Grease 24 muffin tins.
When oats have soaked for 1 hour, add eggs, brown sugar, and applesauce. Mix thoroughly.
In another bowl, whisk together flour, salt, baking powder, baking soda, nutmeg, and cinnamon. Add to the milk mixture, stirring until just combined (don't overmix!). Gently fold in the raspberries and chocolate chips.
Fill the muffin tins 2/3 full. Sprinkle with a little brown sugar, if desired. Bake 18 minutes, until the tops are light golden brown and spring back when touched. Remove from the oven and allow to cool in the tins.