Local registries are ignored when using --override-input

[rennsax]

Describe the bug

I usually set the user level flake registry for nixpkgs so I can use --override-input nixpkgs flake:nixpkgs to stick to the same rev of nixpkgs in all projects. However these days Nix is ignoring my user level registry.

Steps To Reproduce

$ nix registry list | grep '^user'
nix registry list | grep '^user'
user   flake:flake-utils path:/nix/store/01x5k4nlxcpyd85nnr0b9gm89rm8ff4x-source?lastModified=1731533236&narHash=sha256-l0KFg5HjrsfsO/JpG%2Br7fRrqm12kzFHyUHqHCVpMMbI%3D&rev=11707dc2f618dd54ca8739b309ec4fc024de578b
user   flake:nix-darwin path:/nix/store/7yzvsk7hx95ff64qpwfgm98jpyy3ycl8-source?lastModified=1746708654&narHash=sha256-GeC99gu5H6%2BAjBXsn5dOhP4/ApuioGCBkufdmEIWPRs%3D&rev=6cb36e8327421c61e5a3bbd08ed63491b616364a
user   flake:nixpkgs path:/nix/store/yhc8a0a2mvbp8fp53l57i3d5cnz735fc-source?lastModified=1746576598&narHash=sha256-FshoQvr6Aor5SnORVvh/ZdJ1Sa2U4ZrIMwKBX5k2wu0%3D&rev=b3582c75c7f21ce0b429898980eddbbf05c68e55
$ nix flake lock --override-input nixpkgs flake:nixpkgs --override-input flake-utils flake:flake-utils
• Updated input 'nixpkgs':
    'github:NixOS/nixpkgs/b3582c75c7f21ce0b429898980eddbbf05c68e55?narHash=sha256-FshoQvr6Aor5SnORVvh/ZdJ1Sa2U4ZrIMwKBX5k2wu0%3D' (2025-05-07)
  → 'github:NixOS/nixpkgs/2e1da60850ce8159db9654a969c2c683f41c18b5?narHash=sha256-/2jlDI5%2BDfAbxdluamyRsORHueBYUiQh%2BaK/kshSvmE%3D' (2025-05-12)

Expected behavior

flake:nixpkgs should be resolved to b3582c75c7f21ce0b429898980eddbbf05c68e55 so flake.lock should not be modified.

Metadata

nix-env (Nix) 2.28.3

Additional context

#13156 (comment)

Probably related to #13144 (if it is, I'll close this issue)

Checklist

• checked latest Nix manual (source)
• checked open bug issues and pull requests for possible duplicates

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[sedlund]

nix registry list
user   flake:nixpkgs-master github:nixos/nixpkgs/master
system flake:nixpkgs path:/nix/store/jy9gf9bzmz2axsjrirbi90mbfdkd8bcc-source

 nix --version
nix (Nix) 2.28.3

 nix flake show github:numtide/treefmt-nix --override-input nixpkgs nixpkgs
error:
       … while updating the lock file of flake 'github:numtide/treefmt-nix/020cb423808365fa3f10ff4cb8c0a25df35065a3?narHash=sha256-XgxghfND8TDypxsMTPU2GQdtBEsHTEc3qWE6RVEk8O0%3D'

       … while updating the flake input 'nixpkgs'

       error: cannot find flake 'flake:nixpkgs' in the flake registries

lix works as expected

lix --version
nix (Lix, like Nix) 2.91.1

lix flake show github:numtide/treefmt-nix --override-input nixpkgs nixpkgs
warning: not writing modified lock file of flake 'github:numtide/treefmt-nix':
• Updated input 'nixpkgs':
    'github:nixos/nixpkgs/507b63021ada5fee621b6ca371c4fca9ca46f52c' (2025-04-23)
  → 'path:/nix/store/jy9gf9bzmz2axsjrirbi90mbfdkd8bcc-source?lastModified=0&narHash=sha256-618RRHMo5zgmLkLf5ZQqb2ObrOkWVQzr6L1ritQxoJ0%3D' (1970-01-01)
github:numtide/treefmt-nix/020cb423808365fa3f10ff4cb8c0a25df35065a3
├───checks
│   ├───aarch64-darwin
│   │   ├───empty-config omitted (use '--all-systems' to show)
│   │   ├───examples omitted (use '--all-systems' to show)
│   │   ├───formatter-actionlint omitted (use '--all-systems' to show)
│   │   ├───formatter-alejandra omitted (use '--all-systems' to sho
...