Come to find out there are three hex files you need using AVRDUDE, the main program hex file and lfuse and hfuse configure memory hex files. Most of the time I just copy with a universal programmer simple one click but this time it the programmer was broken. So with the usbtiny was a simple connection to the ISP bus.
Here is my redesign of the Clock-it Kit, note there is no ISP connector so programming it in circuit is not possible.
Find and test communications to chip
sudo avrdude -c usbtiny -p m328p
sudo avrdude -c usbtiny -p m328p -e
Burn Main Hex file program
sudo avrdude -c usbtiny -p m328p -U flash:w:clockit-v11.hex
sudo avrdude -c usbtiny -p m328p -U lfuse:w:0xe6:m -U hfuse:w:0xdf:m