Position two oven racks in the upper third and lower third of the oven and preheat to 350°F [175°C]. Cover two baking sheets with parchment paper.
In a large bowl, whisk together the whole wheat flour, baking powder, baking soda, and salt. Set aside.
In the bowl of a stand mixer fitted with the paddle attachment (or in a large mixing bowl, if you’re using a handheld mixer), cream the butter and cane sugar together until fluffy, about 3 minutes. Add the honey and mix to combine.
Add the eggs, one at a time, beating well after each addition. Stop the mixer and scrape down the sides of the bowl. Add the vanilla and mix well. Using a microplane, zest the clementines (or orange) over the bowl so you catch all the aromatic oils along with the zest. Add the flour mixture and mix to combine. Add the chocolate chunks (or chopped chocolate) and stir one last time to incorporate.
Using a 1½ tbsp [20 ml] mini ice cream scoop, scoop the cookie dough into balls and place 12 balls 2 inches [5 centimeters] apart on each of the parchment paper-lined baking sheets. Bake the cookies for 9 to 11 minutes, rotating the baking sheets once halfway through the baking time (moving the sheet that was on top to the bottom rack, and the bottom sheet to the top rack). When done, the cookies should be light brown around the edges but still soft in the center. Let the cookies cool on the baking sheets for 10 minutes, then transfer to wire racks to cool completely.
When the baking sheets are cool, portion out the remaining cookies and bake, or freeze on the baking sheets and transfer to airtight freezer bags for later enjoyment.
Serve freshly baked cookies when just cool enough to handle or, if you serve them later, reheated for 5 minutes in a low oven so they become as gooey as freshly baked again. They’re also delicious served at room temperature, of course!
Keep the cooled cookies in an airtight container at room temperature for up to 4 days, in the refrigerator for up to a week, or in the freezer, for up to a month. Portioned unbaked cookies will keep in airtight freezer bags for up to 6 months. To bake frozen cookie dough balls, place on parchment paper-lined baking sheets and bake directly from frozen in a 350°F [175°C] oven for 12 to 13 minutes.