We currently have the confusing situation that the buildInputs attribute gets passed to the builder via the nativeBuildInputs environment variable:

$ nix-shell '<nixpkgs>' -A pan
[nix-shell:~]$ echo $buildInputs 

[nix-shell:~]$ echo $nativeBuildInputs 
/nix/store/aprw7bdaydpxcv6j3wlr9bnr2s061gq6-pkg-config-0.23 /nix/store/75kv0ac0zn6sxypqh4anwwfdmm3bcw35-gtk+-2.24.24 ...

(Pan declares a buildInputs attribute.)

Also, "native" is somewhat ambiguous: native to the build machine, or native to the target machine? However the GNU terminology (build and host) is not really better.

Maybe it would be better to always use buildInputs for the native (build machine) dependencies, and something like targetBuildInputs for the cross-built dependencies. Or not use buildInputs in setup.sh at all and use nativeBuildInputs and targetBuildInputs to prevent confusion.

Ping @viric