Perhaps you checked out an old version? I just checked and there's a $nixroot/BUILDING_AMD64 file, provided you did the check out at $nixroot.
This is what the file has: cd /sys/src objtype=386 mk libs cd ape/lib mk install cd /sys/src objtype=amd64 mk install BTW, for building the nix kernel just go to /sys/src/nix and mk. It will require amd64 binaries and libraries at /amd64. hth