Preheat the oven to 350 degrees F and line muffin tins with cupcake papers.
In a medium bowl, mix the flour, flaxseed, salt, baking powder and baking soda. Set this aside.
In a food processor, add the prunes and apple sauce and blitz them until the mixture is the texture of sticky applesauce with no big lumps of prune left. You will get about 1 2/3 cup of the puree.
In another medium bowl add the prune and apple sauce puree and mix in the honey, melted butter and brown sugar with a wooden spoon.
Add the egg to the wet mixture and stir well to combine.
When all the wet ingredients are well mixed, including the milk, add the flour mixture and stir until the dry ingredients just disappear into the wet mixture. Use as few turns of the spoon as you can. Over mixing will give you tough muffins.
Spoon muffin batter into lined muffin tins. I use a cookie scooper for the mini muffins and a larger ice cream scoop for the regular muffins. Fill the papers to about 3/4 full.
Bake at 350 degrees F for 12-14 minutes for the mini muffins and 15-18 minutes for the larger muffins. A toothpick will come out clean when inserted to test when they are done.