In a large mixing bowl, cream together the butter, granulated sugar, and brown sugar until light and fluffy.

Beat in the eggs, one at a time. Add the lemon zest, thyme, and vanilla extract, and mix well.

In a separate bowl, whisk together the flour, baking soda, baking powder, and salt.

Gradually mix the dry ingredients into the wet ingredients until just combined.

Fold in the chocolate chunks.

Chill the dough in the refrigerator for at least 30 minutes.

Preheat oven to 350°F (175°C). Line baking sheets with parchment paper.

Scoop dough into balls (about 2 tbsp each) and place them 2 inches apart on the prepared baking sheets.

Sprinkle a pinch of flaky sea salt on top of each dough ball.

Bake for 10-12 minutes, or until the edges are golden and centers are set but soft.

Let cookies cool on the baking sheet for 5 minutes before transferring to a wire rack to cool completely.