Heat oven to 425 degrees. Cover 2 baking sheets with parchment paper, set aside.
In a large bowl, whisk together sugar, peanut butter, agave nectar, and milk.
Add the vanilla and oil, whisk to combine.
Add the espresso powder, whisk until well combined.
Stir in the flour, baking soda, salt, flax seed, and wheat germ with a rubber spoon/spatula.
Stir in the oats, pecans, and chocolate chips.
Drop 1 1/2 Tablespoon sized balls of dough onto prepared baking sheets (or use a small cookie scoop), 12 per sheet.
Bake for 6 minutes. Remove from the oven, and let cool on baking sheet for 10 minutes. Transfer cookies to a cooling rack and allow to cool completely.
Notes
These cookies are very soft, and will appear to not be cooked. Don't let that fool you, they will stiffen up as they cool.