git diff call fails, ".../default.nix" is outside repository at "/repo/path"

[colemickens]

nix-update \
--flake \
packages.x86_64-linux.foot \
--version \
branch=master \
--commit \
--override-filename \
./pkgs/foot/metadata.nix

results in:

[the nix expr that nix-update evals + prints is omitted, except the last line of the output here:]
$ git diff --color=never --word-diff=porcelain -- /nix/store/hhwdvcdgz7qz2prms49lr1h82v5qagxp-source/pkgs/foot/default.nix
fatal: /nix/store/hhwdvcdgz7qz2prms49lr1h82v5qagxp-source/pkgs/foot/default.nix: '/nix/store/hhwdvcdgz7qz2prms49lr1h82v5qagxp-source/pkgs/foot/default.nix' is outside repository at '/home/cole/code/nixpkgs-wayland
[traceback omitted]

(note this is not with master of nixpkgs-wayland, but a branch where I'm experimenting with nix-update instead of my old bespoke update script)

Not quite sure what's going on here? I'm passing a relative path for the file for it to try and update, I'm not doing anything to make an out of repo reference, as far as I can tell.