But you haven’t loaded the firmware.
This is implausible because I don’t believe LEDs and beeper would work with with no firmware uploaded.
Anyway, I followed the steps and flashed Arduino with v2.0 sketch (there is no v2.2 sketch in the repository).
Still same, clock boots up, all digits in all tubes are on immediately, LEDs are on/changing colors, clock plays a tune from ‘Pink panter’ and this is it.