bug: neovim config fails to run setup() on some plugins

Are you following the right branch?

[X] My Nixpkgs and Home Manager versions are in sync

Is there an existing issue for this?

[X] I have searched the existing issues

Issue description

I use home-manager (with flake; home-manager follows nixpkgs input) to manage my whole neovim config. I haven't updated my flake for quite some time. I ran nix flake lock --update-input nixpkgs --update-input home-manager

• Updated input 'home-manager':
    'github:nix-community/home-manager/ee5673246de0254186e469935909e821b8f4ec15' (2023-07-20)
  → 'github:nix-community/home-manager/6045b68ee725167ed0487f0fb88123202ba61923' (2023-10-24)
• Updated input 'nixpkgs':
    'github:nixos/nixpkgs/5df4d78d54f7a34e9ea1f84a22b4fd9baebc68d0' (2023-07-20)
  → 'github:nixos/nixpkgs/7c9cc5a6e5d38010801741ac830a3f8fd667a7a0' (2023-10-19)

Opening nvim after switching (sudo nixos-rebuild switch --flake .), the colorscheme did not loaded, then I figured some plugins did not load This is what it looks like when opening the generated init.lua

What I figured out:

Non-plugin configs work, so keymaps.lua, options.lua et cetera work
The plugins exist. Running :lua require('nvim-tree).setup() enables the plugin commands such as :NvimTreeToggle
Some plugins work for some reason, for example, I am able to run :ZenMode

What I ruled out:

I use neovim-nightly-overlay but switching to the flake.lock generated by nix flake lock --update-input neovim-nightly-overlay does not cause conflict

This is my neovim/default.nix

{ config, pkgs, ... }:
let
  luaConfig = [
    ./lua/impatient.lua
    ./lua/options.lua
    ./lua/keymaps.lua
    ./lua/autocommands.lua
    ./lua/cmp.lua
    ./lua/lsp/main.lua
  ];
in
{
  # yes I should move this to programs.neovim.extraPackages (I just realized recently)
  home.packages = with pkgs; [
    gcc

    # Formatters
    nodePackages_latest.prettier # webdev
    stylua                                                              # lua
    shfmt                                                               # sh
    nixpkgs-fmt                                                         # nix
    rustfmt                                                             # rust
    python310Packages.black                                             # python

    # Linters
    statix                                                              # nix
    shellcheck                                                          # sh
    python310Packages.flake8                                            # python

    # Language Servers
    nodePackages_latest.bash-language-server                            # sh
    nil                                                                 # nix
    gopls                                                               # go
    sumneko-lua-language-server                                         # lua
    rust-analyzer                                                       # rust
    haskellPackages.haskell-language-server                             # haskell
    python311Packages.python-lsp-server                                 # python

    nodePackages_latest."@tailwindcss/language-server"                  # tailwind
    nodePackages_latest."@prisma/language-server"                       # prisma
    nodePackages_latest.typescript-language-server                      # js-related grammars
    nodePackages_latest.vscode-langservers-extracted                    # html, css, json, eslint
    nodePackages_latest.volar                                           # vue
    # emmet-ls                                                            # html snippets
  ];

  xdg.configFile."nvim/lua/lsp" = {
    source = ./lua/lsp;
    recursive = true;
  };

  programs.neovim = {
    enable = true;
    package = pkgs.neovim-nightly;
    defaultEditor = true;
    vimAlias = true;
    withNodeJs = true;
    withPython3 = true;
    withRuby = true;

    extraLuaConfig =
      builtins.concatStringsSep "\n"
        (map builtins.readFile luaConfig);

    plugins = with pkgs.vimPlugins; [
      plenary-nvim
      impatient-nvim
      nvim-web-devicons

      # nvim-tree
      {
        plugin = nvim-tree-lua;
        type = "lua";
        config = builtins.readFile ./lua/nvim-tree.lua;
      }
      # lualine
      {
        plugin = lualine-nvim;
        type = "lua";
        config = builtins.readFile ./lua/lualine.lua;
      }
      # toggleterm
      {
        plugin = toggleterm-nvim;
        type = "lua";
        config = builtins.readFile ./lua/toggleterm.lua;
      }
      # indent-blankline
      {
        plugin = indent-blankline-nvim;
        type = "lua";
        config = builtins.readFile ./lua/indentline.lua;
      }
      # autopairs
      {
        plugin = nvim-autopairs;
        type = "lua";
        config = builtins.readFile ./lua/autopairs.lua;
      }
      # nvim-surround
      {
        plugin = nvim-surround;
        type = "lua";
        config = builtins.readFile ./lua/nvim-surround.lua;
      }
      # treesj
      {
        plugin = treesj;
        type = "lua";
        config = builtins.readFile ./lua/treesj.lua;
      }
      # persistence-nvim
      {
        plugin = persistence-nvim;
        type = "lua";
        config = ''
          require("persistence").setup()
        '';
      }
      # which-key
      {
        plugin = which-key-nvim;
        type = "lua";
        config = builtins.readFile ./lua/whichkey.lua;
      }

      # Cmp
      nvim-cmp
      cmp-buffer
      cmp-path
      cmp_luasnip
      cmp-nvim-lsp
      cmp-nvim-lua

      # Snippets
      luasnip
      friendly-snippets

      # LSP
      # nvim-lspconfig
      {
        plugin = nvim-lspconfig;
        type = "lua";
        config = ''
          require('lspconfig').nil_ls.setup({
              cmd = { "${pkgs.nil}/bin/nil" }
          })
          require('lspconfig').lua_ls.setup({
              cmd = { "${pkgs.lua-language-server}/bin/lua-language-server" }
          })
        '';
      }
      # typescript-nvim
      {
        plugin = typescript-nvim;
        type = "lua";
        config = builtins.readFile ./lua/typescript-nvim.lua;
      }
      # crates.nvim
      {
        plugin = crates-nvim;
        type = "lua";
        config = builtins.readFile ./lua/crates.nvim.lua;
      }
      # null-ls
      {
        plugin = null-ls-nvim;
        type = "lua";
        config = builtins.readFile ./lua/null-ls.lua;
      }
      # refactoring
      {
        plugin = refactoring-nvim;
        type = "lua";
        config = builtins.readFile ./lua/refactoring.lua;
      }

      # Telescope
      {
        plugin = telescope-nvim;
        type = "lua";
        config = builtins.readFile ./lua/telescope.lua;
      }

      # Treesitter
      {
        plugin = nvim-treesitter.withAllGrammars;
        type = "lua";
        config = builtins.readFile ./lua/treesitter.lua;
      }

      # telescope-manix
      telescope-manix

      # gitsigns
      {
        plugin = gitsigns-nvim;
        type = "lua";
        config = builtins.readFile ./lua/gitsigns.lua;
      }
      # comment-nvim
      {
        plugin = comment-nvim;
        type = "lua";
        config = builtins.readFile ./lua/comment.lua;
      }

      # nvim-ts-context-commentstring 
      #   config is integrated with treesitter and comment-nvim
      nvim-ts-context-commentstring

      # nvim-ts-autotag
      {
        plugin = nvim-ts-autotag;
        type = "lua";
        config = builtins.readFile ./lua/nvim-ts-autotag.lua;
      }

      # trouble-nvim
      {
        plugin = trouble-nvim;
        type = "lua";
        config = builtins.readFile ./lua/trouble.lua;
      }
      # todo-comments
      {
        plugin = todo-comments-nvim;
        type = "lua";
        config = builtins.readFile ./lua/todo-comments.lua;
      }
      # leap
      {
        plugin = leap-nvim;
        type = "lua";
        config = builtins.readFile ./lua/leap.lua;
      }
      # wilder
      {
        plugin = wilder-nvim;
        type = "lua";
        config = builtins.readFile ./lua/wilder.lua;
      }
      {
        plugin = markdown-preview-nvim;
        type = "lua";
        config = builtins.readFile ./lua/markdownpreview.lua;
      }
      # zen mode
      {
        plugin = zen-mode-nvim;
        type = "lua";
        config = builtins.readFile ./lua/zen-mode.lua;
      }
      # twilight-nvim
      {
        plugin = twilight-nvim;
        type = "lua";
        config = builtins.readFile ./lua/twilight.lua;
      }
      # nvim-highlight-colors
      {
        plugin = nvim-highlight-colors;
        type = "lua";
        config = builtins.readFile ./lua/nvim-highlight-colors.lua;
      }
      # nvim-lastplace
      {
        plugin = nvim-lastplace;
        type = "lua";
        config = builtins.readFile ./lua/nvim-lastplace.lua;
      }
      # kmonad-vim (kbd syntax highlighting)
      kmonad-vim

      # Colorschemes
      {
        plugin = kanagawa-nvim;
        # plugin = tokyonight-nvim;
        # plugin = rose-pine;
        type = "lua";
        config = builtins.readFile ./lua/colorschemes/kanagawa.lua + ''
          local status_ok, _ = pcall(vim.cmd, "colorscheme " .. "kanagawa")
          if not status_ok then
              return
          end
        '' + builtins.readFile ./lua/colorschemes/setbgtotransparent.lua;
      }
    ];
  };
}

This is probably not a bug but a breaking change that I missed to patch on my config (?)

Maintainer CC

No response

System information

- system: `"x86_64-linux"`
 - host os: `Linux 6.1.38, NixOS, 23.11 (Tapir), 23.11.20230720.5df4d78`
 - multi-user?: `yes`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.15.1`
 - nixpkgs: `/nix/var/nix/profiles/per-user/root/channels/nixos`

nix-community / home-manager