In a medium bowl, sift together the flour(s), baking soda, nutmeg, cinnamon and salt.
In a small bowl, mix the ground flax seeds with the warm water. Let that sit for a bit and then stir it after a few minutes until the mixture becomes a bit thick.
In a small food processor*, pulse the carrots until they're "grated" consistency (i.e., not pureed).
Add in the butter, brown sugar, vanilla, and the flax seed mixture. Pulse until combined, scraping the edges a few times as you go.
Gradually add the flour mixture into the food processor. Pulse until just combined, don't over mix.
Scrape your batter into a bowl (i.e., the one you just used for the flour). Refrigerate for 30 minutes.**
Preheat your oven to 375 degrees and line a baking sheet with parchment paper.
Remove from the refrigerator and stir in oats, walnuts and chocolate chips.
Using a tablespoon, scoop batter into balls and place on cookie sheet at least a few inches apart.
Bake for 10-12 minutes until golden brown and the edges become slightly crisp.