Stir together the flours, spices, baking soda, baking powder and salt in a medium mixing bowl.
In a small bowl, combine the ground chia seeds with 3 tablespoons of water and mix well. Set aside to gel.
With a baking spatula or wooden spoon, cream together the sugar and coconut oil in a large mixing bowl. Add the molasses, apple sauce and gelled chia and mix.
Pour the dry mixture into the wet and, using a baking spatula, mix until everything is fully incorporated and you have a thick batter. Cover the bowl with plastic wrap and place in the fridge to chill for an hour.
When the dough is almost done chilling, preheat the oven to 325ºF and line a baking sheet with parchment paper.
Roll the chilled dough into little balls (about 1 tablespoon of dough per ball). You can roll the dough in sugar if you desire. Place the balls about 2 inches apart on the baking sheet and press down lightly with a dampened fork. Bake for about 12 minutes.
Remove the cookies from the oven and allow them to cool for about 2 minutes on the baking sheet before transferring them to a cooling wrack to cool completely.