Add almond flour, coconut flour, arrowroot powder, salt, baking soda and xanthan gum to a medium bowl.
Whisk until thoroughly combined and set aside.Cream butter in a large bowl with an electric mixer, 2-3 minutes.
Add in sweetener and molasses (optional), and continue to beat until thoroughly mixed and much of the sweetener has dissolved.
Add in vanilla extract and egg, mixing until just incorporated.
The mixture will appear slightly 'broken' (i.e.
not thoroughly smooth).
With your mixer on low, add in half of your flour mixture- mixing until just incorporated.
Mix in the rest.Fold in chocolate and pecan bits.
Cover with cling film and refrigerate for 1 hour.Preheat oven to 350°F/180°C and line a baking tray with parchment paper (if you use a silpat baking mat they won't spread much, if at all).Divide cookie dough into 12, form into rounds and flatten them to 2 1/2 inches in diameter.
The cookies will spread somewhat during baking, but you still need to pre-shape them slightly.
Place cookie dough on the prepared baking tray (or freeze, see notes).
Bake for 12-13 minutes, flipping tray around and sprinkling with flakey sea salt half way through, until just set (but still soft to touch).Allow the cookies to cool completely on the trays.
Store in an airtight container for up to three days.