If you are running linux, you first need to load the at91 kernel driver:
> insmod driver/at91.ko

Once that's loaded (or you are using OSX):
> ./sam7
response = 0d0a
it begins
sam7> set_clock
sam7> unlock_regions
unlocking page 0: done
unlocking page 1: done


sam7> manual_flash test.bin 
>