Short answer:
J1 is the in-circuit programming header placeholder, but it hasn’t been wired to the ATmega’s ISP signals yet.
Optionally, we can swap
J1 to the standard keyed 2x3 AVR ISP footprint for tooling compatibility:
2x3 Pin Header.
Want me to wire
J1 per the mapping above and, if you prefer, replace it with a keyed 2x3 header?