Nix doesn't recognize removal of flake = false from inputs

[shlevy]

Describe the bug

When a flake input is locked at flake = false, removing the flake = false setting from the flake.nix does not cause Nix to update the flake lock nor fetch the flake's inputs.

Steps To Reproduce

Given flake.nix:

{
  description = "A very basic flake";

  inputs = {
    iohk-nix = {
      url = "github:input-output-hk/iohk-nix";
      flake = false;
    };
  };

  outputs = { self, nixpkgs }: {

    packages.x86_64-linux.hello = nixpkgs.legacyPackages.x86_64-linux.hello;

    packages.x86_64-linux.default = self.packages.x86_64-linux.hello;

  };
}

flake.lock:

{
  "nodes": {
    "iohk-nix": {
      "flake": false,
      "locked": {
        "lastModified": 1685727458,
        "narHash": "sha256-c/pkFYCfzpRb6W2OOKE+EOzOlcw+96vwJGGg8Ir9Qfk=",
        "owner": "input-output-hk",
        "repo": "iohk-nix",
        "rev": "02f42375ee5c2bab1640f14c6389b7e91bbfec8b",
        "type": "github"
      },
      "original": {
        "owner": "input-output-hk",
        "repo": "iohk-nix",
        "type": "github"
      }
    },
    "nixpkgs": {
      "locked": {
        "lastModified": 1686582075,
        "narHash": "sha256-vtflsfKkHtF8IduxDNtbme4cojiqvlvjp5QNYhvoHXc=",
        "owner": "NixOS",
        "repo": "nixpkgs",
        "rev": "7e63eed145566cca98158613f3700515b4009ce3",
        "type": "github"
      },
      "original": {
        "id": "nixpkgs",
        "type": "indirect"
      }
    },
    "root": {
      "inputs": {
        "iohk-nix": "iohk-nix",
        "nixpkgs": "nixpkgs"
      }
    }
  },
  "root": "root",
  "version": 7
}

1. Remove flake = false line
2. Run nix flake lock
3. If in git, see warning about dirty tree, but flake.lock is unchanged.

Expected behavior

A flake.lock like (this one obtained by removing the entry, locking, then adding the entry and locking):

{
  "nodes": {
    "blst": {
      "flake": false,
      "locked": {
        "lastModified": 1656163412,
        "narHash": "sha256-xero1aTe2v4IhWIJaEDUsVDOfE77dOV5zKeHWntHogY=",
        "owner": "supranational",
        "repo": "blst",
        "rev": "03b5124029979755c752eec45f3c29674b558446",
        "type": "github"
      },
      "original": {
        "owner": "supranational",
        "repo": "blst",
        "rev": "03b5124029979755c752eec45f3c29674b558446",
        "type": "github"
      }
    },
    "iohk-nix": {
      "inputs": {
        "blst": "blst",
        "nixpkgs": "nixpkgs",
        "secp256k1": "secp256k1",
        "sodium": "sodium"
      },
      "locked": {
        "lastModified": 1685727458,
        "narHash": "sha256-c/pkFYCfzpRb6W2OOKE+EOzOlcw+96vwJGGg8Ir9Qfk=",
        "owner": "input-output-hk",
        "repo": "iohk-nix",
        "rev": "02f42375ee5c2bab1640f14c6389b7e91bbfec8b",
        "type": "github"
      },
      "original": {
        "owner": "input-output-hk",
        "repo": "iohk-nix",
        "type": "github"
      }
    },
    "nixpkgs": {
      "locked": {
        "lastModified": 1684171562,
        "narHash": "sha256-BMUWjVWAUdyMWKk0ATMC9H0Bv4qAV/TXwwPUvTiC5IQ=",
        "owner": "nixos",
        "repo": "nixpkgs",
        "rev": "55af203d468a6f5032a519cba4f41acf5a74b638",
        "type": "github"
      },
      "original": {
        "owner": "nixos",
        "ref": "release-22.11",
        "repo": "nixpkgs",
        "type": "github"
      }
    },
    "nixpkgs_2": {
      "locked": {
        "lastModified": 1686582075,
        "narHash": "sha256-vtflsfKkHtF8IduxDNtbme4cojiqvlvjp5QNYhvoHXc=",
        "owner": "NixOS",
        "repo": "nixpkgs",
        "rev": "7e63eed145566cca98158613f3700515b4009ce3",
        "type": "github"
      },
      "original": {
        "id": "nixpkgs",
        "type": "indirect"
      }
    },
    "root": {
      "inputs": {
        "iohk-nix": "iohk-nix",
        "nixpkgs": "nixpkgs_2"
      }
    },
    "secp256k1": {
      "flake": false,
      "locked": {
        "lastModified": 1683999695,
        "narHash": "sha256-9nJJVENMXjXEJZzw8DHzin1DkFkF8h9m/c6PuM7Uk4s=",
        "owner": "bitcoin-core",
        "repo": "secp256k1",
        "rev": "acf5c55ae6a94e5ca847e07def40427547876101",
        "type": "github"
      },
      "original": {
        "owner": "bitcoin-core",
        "ref": "v0.3.2",
        "repo": "secp256k1",
        "type": "github"
      }
    },
    "sodium": {
      "flake": false,
      "locked": {
        "lastModified": 1675156279,
        "narHash": "sha256-0uRcN5gvMwO7MCXVYnoqG/OmeBFi8qRVnDWJLnBb9+Y=",
        "owner": "input-output-hk",
        "repo": "libsodium",
        "rev": "dbb48cce5429cb6585c9034f002568964f1ce567",
        "type": "github"
      },
      "original": {
        "owner": "input-output-hk",
        "repo": "libsodium",
        "rev": "dbb48cce5429cb6585c9034f002568964f1ce567",
        "type": "github"
      }
    }
  },
  "root": "root",
  "version": 7
}

nix --version output

nix (Nix) 2.16.1

Additional context

Add any other context about the problem here.

Priorities

Add 👍 to issues you find important.

[shlevy]

This seems to also impact recursive updates: If A depends on B, and B has a flake = false dependency on C, then I update B to have a flake = true dependency on C, then updating A's dependency on B requires removing and re-adding B (Otherwise I get an error like "input 'iogx/iohk-nix' has an override for a non-existent input 'nixpkgs'")

[nixos-discourse]

This issue has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/2023-06-16-nix-team-meeting-minutes-63/29316/1