From 10254b11c727c139794d4d3b555c24562d9847ba Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sat, 23 May 2026 18:41:22 +1000
Subject: [PATCH 01/11] Corrected langpackage installation

---
 .commandcode/taste/taste.md |  9 -------
 .gitignore                  |  2 ++
 flake.nix                   | 52 ++++++++++++++++++-------------------
 plugin/10_keymap.lua        |  4 +--
 4 files changed, 30 insertions(+), 37 deletions(-)
 delete mode 100644 .commandcode/taste/taste.md

diff --git a/.commandcode/taste/taste.md b/.commandcode/taste/taste.md
deleted file mode 100644
index 54e4488..0000000
--- a/.commandcode/taste/taste.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# nix
-- For R.nvim in the Nix wrapper, both RNVIM_COMPLDIR (C server compilation) and a writable R_LIBS_USER directory (nvimcom R package installation) must be configured — fixing only one leaves permission errors in the other. Confidence: 0.65
-- For R.nvim writable directories (RNVIM_COMPLDIR, R_LIBS_USER, TMPDIR), prefer project-local paths (e.g., $PWD/.Rlibs) over global cache paths — the cache approach may let the build succeed but still fail at runtime. Confidence: 0.70
-- Do not use lib.mkDefault on values consumed by lib.optionals or other boolean-checking functions — mkDefault wraps values in a priority set that fails "expected a Boolean" at evaluation time. Use plain booleans for inline conditionals, reserving mkDefault for module options resolved by the merge system. Confidence: 0.70
-
-# Taste (Continuously Learned by [CommandCode][cmd])
-
-[cmd]: https://commandcode.ai/
-
diff --git a/.gitignore b/.gitignore
index 8474af7..e402ff0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,5 @@
 *.R
 .Rlibs
 .nvimcom
+.commandcode
+.commandcode/
diff --git a/flake.nix b/flake.nix
index 2780328..a19f7dc 100644
--- a/flake.nix
+++ b/flake.nix
@@ -1,4 +1,4 @@
-# Copyright (c) 2026 Daniel
+# Copyright (c) 2026 BirdeeHub & Daniel
 # Licensed under the MIT license
 {
   description = "Daniel's NixCats";
@@ -39,6 +39,25 @@
     wrappers,
     ...
   } @ inputs: let
+    langPackages = pkgs: {
+      python = with pkgs.python3Packages; [
+        duckdb
+        polars
+      ];
+      r = (with pkgs.rpkgs.rPackages; [
+        arrow
+        broom
+        data_table
+        janitor
+        styler
+        pkgs.nvimcom
+      ]) ++ [ pkgs.nvimcom ];
+      julia = [
+        "DataFramesMeta"
+        "QuackIO"
+      ];
+    };
+
     mkWrapperConfig = pkgs: {
       cats = {
         clickhouse = false;
@@ -52,11 +71,7 @@
         r = true;
       };
       settings = {
-        lang_packages = {
-          python = [];
-          r = [];
-          julia = [];
-        };
+        lang_packages = langPackages pkgs;
       };
       binName = "vv";
     };
@@ -125,27 +140,13 @@
         pkgs = mkPkgs system;
         nvimPkg = wrapperSettings pkgs;
 
-        pythonPkgs = with pkgs.python3Packages; [
-          duckdb
-          polars
-        ];
-
-        rPkgs = (with pkgs.rpkgs.rPackages; [
-          arrow
-          broom
-          data_table
-          janitor
-          languageserver
-          styler
-        ]) ++ [ pkgs.nvimcom ];
-
-        juliaPkgs = ["DataFramesMeta" "QuackIO"];
+        langPkgs = langPackages pkgs;
 
         pythonPackages = let
           python_packages_fn =
             if pkgs ? basePythonPackages
-            then ps: pkgs.basePythonPackages ps ++ pythonPkgs
-            else _: pythonPkgs;
+            then ps: pkgs.basePythonPackages ps ++ langPkgs.python
+            else _: langPkgs.python;
         in
           with pkgs; [
             (python3.withPackages python_packages_fn)
@@ -156,7 +157,7 @@
           ];
 
         rPackages = let
-          r_packages = (pkgs.baseRPackages or []) ++ rPkgs;
+          r_packages = (pkgs.baseRPackages or []) ++ langPkgs.r;
         in
           with pkgs; [
             (rWrapper.override {packages = r_packages;})
@@ -164,13 +165,12 @@
             (quarto.override {extraRPackages = r_packages;})
             air-formatter
             yaml-language-server
-            updateR
             nvimcom
             rnvimserver
           ];
 
         juliaPackages = let
-          julia_with_packages = pkgs.julia-bin.withPackages juliaPkgs;
+          julia_with_packages = pkgs.julia-bin.withPackages langPkgs.julia;
         in [julia_with_packages];
 
         markdownPackages = with pkgs; [
diff --git a/plugin/10_keymap.lua b/plugin/10_keymap.lua
index ebbebf0..5682b93 100644
--- a/plugin/10_keymap.lua
+++ b/plugin/10_keymap.lua
@@ -37,7 +37,7 @@ _G.Config.leader_group_clues = {
   { mode = 'x', keys = '<Leader>l',  desc = '+LSP' },
   { mode = 'x', keys = '<Leader>r',  desc = '+R' },
   { mode = 'n', keys = '<Leader>z',  desc = '+ZK' },
-  { mode = 'n', keys = '<Leader>zr',  desc = '+Reviews' },
+  { mode = 'n', keys = '<Leader>zr', desc = '+Reviews' },
   { mode = 'x', keys = '<leader>a',  desc = '+AI' },
 }
 
@@ -144,7 +144,7 @@ nmap_leader('gc', '<Cmd>Git commit<CR>', 'Commit')
 nmap_leader('gC', '<Cmd>Git commit --amend<CR>', 'Commit amend')
 nmap_leader('gd', '<Cmd>Git diff<CR>', 'Diff')
 nmap_leader('gD', '<Cmd>Git diff -- %<CR>', 'Diff buffer')
-nmap_leader('gg', '<Cmd>lua require("neogit").open()<CR>', 'Git tab')
+nmap_leader("gg", "<cmd>Neogit<cr>", "Open Neogit UI")
 nmap_leader('gl', '<Cmd>' .. git_log_cmd .. '<CR>', 'Log')
 nmap_leader('gL', '<Cmd>' .. git_log_cmd .. ' --follow -- %<CR>', 'Log buffer')
 nmap_leader('go', '<Cmd>lua MiniDiff.toggle_overlay()<CR>', 'Toggle overlay')

From a0ba90c4d2ff20c4deb961b839b8c8e7518f4268 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sat, 23 May 2026 20:15:23 +1000
Subject: [PATCH 02/11] refactor package installation

---
 README.md                                | 247 +++++++++++++++++++++++
 flake.lock                               |  28 ++-
 flake.nix                                | 109 ++++------
 modules/module/settings/cat-packages.nix | 109 ++++++++++
 modules/module/settings/cats.nix         |   2 +
 modules/module/settings/runtime-path.nix |  33 ---
 modules/module/specs/deps.nix            |  96 ++-------
 modules/neovim.nix                       |   2 +-
 8 files changed, 433 insertions(+), 193 deletions(-)
 create mode 100644 README.md
 create mode 100644 modules/module/settings/cat-packages.nix
 delete mode 100644 modules/module/settings/runtime-path.nix

diff --git a/README.md b/README.md
new file mode 100644
index 0000000..c50d03e
--- /dev/null
+++ b/README.md
@@ -0,0 +1,247 @@
+# nvimConfig
+
+Modular Neovim wrapper config. Defines a wrapped `vv` binary with per-category packages, plugins, and environment variables. Available as NixOS module, Home Manager module, or single-starflake import.
+
+## Quick start (imported into another flake)
+
+```nix
+{
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+    rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
+    fran = {
+      url = "github:dwinkler1/fran";
+      inputs.nixpkgs.follows = "rixpkgs";
+    };
+    nvimConfig = {
+      url = "github:dwinkler1/nvimConfig";
+      inputs = {
+        nixpkgs.follows = "nixpkgs";
+        rixpkgs.follows = "rixpkgs";
+        fran.follows = "fran";
+      };
+    };
+  };
+
+  outputs = { self, nixpkgs, nvimConfig, ... } @ inputs: let
+    systems = ["aarch64-darwin" "x86_64-linux" "aarch64-linux"];
+    forAllSystems = nixpkgs.lib.genAttrs systems;
+  in {
+    packages = forAllSystems (system: let
+      pkgs = import nixpkgs {
+        inherit system;
+        config.allowUnfree = true;
+        overlays = [ nvimConfig.overlays.dependencies ];
+      };
+      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
+        modules = [
+          nvimConfig.wrapperModules.default
+          projectSettings  # see below
+        ];
+      };
+    in {
+      default = evalResult.config.wrap { inherit pkgs; };
+    });
+
+    devShells = forAllSystems (system: let
+      pkgs = import nixpkgs {
+        inherit system;
+        config.allowUnfree = true;
+        overlays = [ nvimConfig.overlays.dependencies ];
+      };
+      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
+        modules = [
+          nvimConfig.wrapperModules.default
+          projectSettings
+        ];
+      };
+      nv = evalResult.config.wrap { inherit pkgs; };
+    in {
+      default = pkgs.mkShell {
+        packages =
+          [ nv ]
+          ++ (evalResult.config.catPkgs.markdown or [])
+          ++ (evalResult.config.catPkgs.nix or []);
+      };
+    });
+  };
+}
+```
+
+## Home Manager module
+
+```nix
+{ inputs, ... }: {
+  home.packages = [
+    (inputs.nvimConfig.homeModules.default { inherit pkgs; })
+    # Or via the overlay:
+    # pkgs.vv
+  ];
+}
+```
+
+## NixOS module
+
+```nix
+{ inputs, ... }: {
+  environment.systemPackages = [
+    (inputs.nvimConfig.nixosModules.default { inherit pkgs; })
+  ];
+}
+```
+
+## Overriding settings
+
+Define a `projectSettings` attrset and pass it as the second module in `evalModules`. Every option in `nvimConfig.wrapperConfigs.default` can be overridden here.
+
+### Categories
+
+Enable only the cats you need. Defaults are listed in `modules/module/settings/cats.nix`.
+
+```nix
+projectSettings = {
+  cats = {
+    python = true;       # enable Python tooling
+    r = false;           # disable R
+    nix = true;
+    lua = false;
+    markdown = false;
+    optional = false;
+    gitPlugins = false;
+  };
+};
+```
+
+### Language packages (overlay extension)
+
+Add Python/R/Julia libraries that get appended to the overlay base packages.
+
+```nix
+projectSettings = {
+  settings.lang_packages = {
+    python = with pkgs.python3Packages; [ pandas numpy ];
+    r = with pkgs.rpkgs.rPackages; [ fixest data_table ];
+    julia = [ "StatsBase" "Plots" ];
+  };
+};
+```
+
+Use `lib.mkForce` to replace rather than append:
+
+```nix
+projectSettings = {
+  settings.lang_packages = {
+    python = pkgs.lib.mkForce (with pkgs.python3Packages; [ polars duckdb ]);
+  };
+};
+```
+
+### Runtime dependencies (per-cat packages)
+
+Override `catPkgs` to add tools that appear in both the wrapper PATH and the devShell. To add always-available packages not gated by any cat, use `runtimePkgs` directly (see next section).
+
+```nix
+projectSettings = {
+  catPkgs = {
+    nix = [ pkgs.nil pkgs.nixfmt ];
+    python = [
+      (pkgs.python3.withPackages (ps: [ ps.pandas ps.duckdb ]))
+      pkgs.ruff
+    ];
+  };
+};
+```
+
+### Direct runtimePkgs override (always-on)
+
+Add packages to `catPkgs.always` for tools that should always be available regardless of other cat toggles.
+
+```nix
+projectSettings = {
+  catPkgs = {
+    always = [ pkgs.git pkgs.curl pkgs.pre-commit ];
+  };
+};
+```
+
+### Runtime env vars
+
+```nix
+projectSettings = {
+  env = {
+    MY_PROJECT_VAR = "some-value";
+  };
+  envDefault = {
+    EDITOR = "vv";
+  };
+};
+```
+
+`env` values are forced; `envDefault` values can be overridden by the user's shell.
+
+### Neovim settings
+
+```nix
+projectSettings = {
+  settings = {
+    colorscheme = "kanagawa";
+    background = "dark";
+    wrapRc = true;
+    config_directory = ./nvim;  # path to init.lua + lua/ dir
+    aliases = [ "v" "nvim" ];   # extra binary names (default: [ "vvim" ])
+  };
+  binName = "nv";               # binary name (default: vv)
+};
+```
+
+## Adding plugins
+
+```nix
+projectSettings = {
+  specs = {
+    extraPlugins = {
+      data = with pkgs.vimPlugins; [
+        telescope-nvim
+        which-key-nvim
+      ];
+    };
+
+    extraLazy = {
+      lazy = true;
+      data = with pkgs.vimPlugins; [ dashboard-nvim ];
+    };
+
+    # Inject Lua config at startup
+    extraLua = {
+      data = pkgs.writeText "extra.lua" ''
+        vim.opt.number = true
+        vim.opt.relativenumber = true
+      '';
+      before = ["INIT_MAIN"];
+    };
+  };
+};
+```
+
+## Architecture
+
+```
+langPackages (flake.nix) ──► settings.lang_packages (module option)
+                                        │
+cats.nix ──► config.cats                │
+                  │                     │
+                  ▼                     ▼
+          cat-packages.nix ──► config.catPkgs.<cat>
+                  │                     │
+          ┌───────┘                     │
+          ▼                             ▼
+   deps.nix (runtimePkgs)       flake.nix (devShells)
+          │                             │
+          ▼                             ▼
+   wrapped vv PATH              nix develop PATH
+```
+
+- **Overlays** (`overlays/`) inject base packages into nixpkgs (rWrapper, quarto, baseRPackages, basePythonPackages).
+- **cat-packages.nix** is the single source of truth for per-category packages. Each list is gated by its cat toggle.
+- **deps.nix** wires `catPkgs` into the wrapper's runtime PATH.
+- **flake.nix** reads `catPkgs` for the devShell. `langPackages` feeds into `settings.lang_packages`.
diff --git a/flake.lock b/flake.lock
index 698ccf9..02745a6 100644
--- a/flake.lock
+++ b/flake.lock
@@ -74,20 +74,19 @@
         "nixpkgs": [
           "rixpkgs"
         ],
-        "rnvimsrc": [
-          "plugins-r"
-        ]
+        "rnvimsrc": "rnvimsrc"
       },
       "locked": {
-        "lastModified": 1778684156,
-        "narHash": "sha256-Z4y1tQfkIsPK4NRxGn668HMDfWxnxNxSJ0CAOOXiIfY=",
+        "lastModified": 1779438909,
+        "narHash": "sha256-1lvv0bdvSVyeCIgeZ7Ws7ffbDFurA5LJscS9dRLHzC8=",
         "owner": "dwinkler1",
         "repo": "r_nvim_nix",
-        "rev": "2f49dfee27886068e2f49cbd54558ce4cc424c82",
+        "rev": "ec17e22ab362a0ddfd6c2e9c5e95d43897a143be",
         "type": "github"
       },
       "original": {
         "owner": "dwinkler1",
+        "ref": "v0.99.4",
         "repo": "r_nvim_nix",
         "type": "github"
       }
@@ -108,6 +107,23 @@
         "type": "github"
       }
     },
+    "rnvimsrc": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1776905071,
+        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
+        "owner": "R-nvim",
+        "repo": "R.nvim",
+        "rev": "582f2af11290ac067e49018db38e12a511325556",
+        "type": "github"
+      },
+      "original": {
+        "owner": "R-nvim",
+        "ref": "v0.99.4",
+        "repo": "R.nvim",
+        "type": "github"
+      }
+    },
     "root": {
       "inputs": {
         "fran": "fran",
diff --git a/flake.nix b/flake.nix
index a19f7dc..cde55df 100644
--- a/flake.nix
+++ b/flake.nix
@@ -11,9 +11,12 @@
     };
     rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
 
-    r-nvim-nix.url = "github:dwinkler1/r_nvim_nix";
-    r-nvim-nix.inputs.rnvimsrc.follows = "plugins-r";
-    r-nvim-nix.inputs.nixpkgs.follows = "rixpkgs";
+    r-nvim-nix = {
+      url = "github:dwinkler1/r_nvim_nix/v0.99.4";
+      inputs = {
+        nixpkgs.follows = "rixpkgs";
+      };
+    };
 
     fran = {
       url = "github:dwinkler1/fran";
@@ -44,14 +47,15 @@
         duckdb
         polars
       ];
-      r = (with pkgs.rpkgs.rPackages; [
-        arrow
-        broom
-        data_table
-        janitor
-        styler
-        pkgs.nvimcom
-      ]) ++ [ pkgs.nvimcom ];
+      r =
+        (with pkgs.rpkgs.rPackages; [
+          arrow
+          broom
+          data_table
+          janitor
+          styler
+        ])
+        ++ [pkgs.nvimcom];
       julia = [
         "DataFramesMeta"
         "QuackIO"
@@ -59,17 +63,6 @@
     };
 
     mkWrapperConfig = pkgs: {
-      cats = {
-        clickhouse = false;
-        gitPlugins = true;
-        julia = false;
-        lua = true;
-        markdown = true;
-        nix = true;
-        optional = false;
-        python = false;
-        r = true;
-      };
       settings = {
         lang_packages = langPackages pkgs;
       };
@@ -97,8 +90,12 @@
     mkPkgs = system:
       import nixpkgs {
         inherit system;
-        config = { allowUnfree = true; };
-        overlays = [ overlayDefs.dependencyOverlay ];
+        config = {allowUnfree = true;};
+        overlays = [
+          overlayDefs.dependencyOverlay
+          inputs.r-nvim-nix.overlays.default
+          inputs.fran.overlays.default
+        ];
       };
 
     module = (import ./modules/neovim.nix) inputs;
@@ -140,56 +137,21 @@
         pkgs = mkPkgs system;
         nvimPkg = wrapperSettings pkgs;
 
-        langPkgs = langPackages pkgs;
-
-        pythonPackages = let
-          python_packages_fn =
-            if pkgs ? basePythonPackages
-            then ps: pkgs.basePythonPackages ps ++ langPkgs.python
-            else _: langPkgs.python;
-        in
-          with pkgs; [
-            (python3.withPackages python_packages_fn)
-            nodejs
-            ruff
-            basedpyright
-            uv
-          ];
-
-        rPackages = let
-          r_packages = (pkgs.baseRPackages or []) ++ langPkgs.r;
-        in
-          with pkgs; [
-            (rWrapper.override {packages = r_packages;})
-            radianWrapper
-            (quarto.override {extraRPackages = r_packages;})
-            air-formatter
-            yaml-language-server
-            nvimcom
-            rnvimserver
-          ];
-
-        juliaPackages = let
-          julia_with_packages = pkgs.julia-bin.withPackages langPkgs.julia;
-        in [julia_with_packages];
-
-        markdownPackages = with pkgs; [
-          python313Packages.pylatexenc
-          quarto
-          zk
-        ];
-
-        shellPackages =
-          [nvimPkg]
-          ++ pkgs.lib.optionals wrapper.config.cats.python pythonPackages
-          ++ pkgs.lib.optionals wrapper.config.cats.r rPackages
-          ++ pkgs.lib.optionals wrapper.config.cats.julia juliaPackages
-          ++ pkgs.lib.optionals wrapper.config.cats.markdown markdownPackages;
+        shellPackages = [nvimPkg]
+          ++ wrapper.config.catPkgs.always or []
+          ++ wrapper.config.catPkgs.python or []
+          ++ wrapper.config.catPkgs.r or []
+          ++ wrapper.config.catPkgs.julia or []
+          ++ wrapper.config.catPkgs.markdown or []
+          ++ wrapper.config.catPkgs.optional or []
+          ++ wrapper.config.catPkgs.external or []
+          ++ wrapper.config.catPkgs.nix or []
+          ++ wrapper.config.catPkgs.lua or []
+          ++ wrapper.config.catPkgs.clickhouse or [];
       in {
         default = pkgs.mkShell {
           name = "vShell";
           packages = shellPackages;
-          nativeBuildInputs = pkgs.lib.optionals wrapper.config.cats.optional [ pkgs.devenv ];
           shellHook = ''
             echo 'I am a NixShell'
             export R_HOME=$(R RHOME)
@@ -223,9 +185,10 @@
             cat version_output.txt >> $out
           fi
         '';
-        module-eval =
-          let _ = wrapper.config;
-          in pkgs.runCommand "check-module-eval" {} ''
+        module-eval = let
+          _ = wrapper.config;
+        in
+          pkgs.runCommand "check-module-eval" {} ''
             echo "Module evaluation successful" > $out
           '';
       }
diff --git a/modules/module/settings/cat-packages.nix b/modules/module/settings/cat-packages.nix
new file mode 100644
index 0000000..3570ff6
--- /dev/null
+++ b/modules/module/settings/cat-packages.nix
@@ -0,0 +1,109 @@
+{
+  config,
+  pkgs,
+  lib,
+  ...
+}:
+let
+  maybe = cat: pkgsList:
+    lib.optionals (config.cats.${cat} or false) pkgsList;
+in
+{
+  options.catPkgs = lib.mkOption {
+    type = lib.types.attrsOf (lib.types.listOf lib.types.package);
+    description = "Per-cat package lists, gated by cat toggles. Single source of truth for runtimeDeps and devShells.";
+  };
+
+  config.catPkgs = {
+    always = maybe "always" (with pkgs; [ ]);
+
+    clickhouse = maybe "clickhouse" (with pkgs; [ clickhouse-lts ]);
+
+    external = maybe "external" (with pkgs; [
+      perl
+      ruby
+      shfmt
+      sqlfluff
+      tree-sitter
+    ]);
+
+    julia = maybe "julia" [
+      (pkgs.julia-bin.withPackages config.settings.lang_packages.julia)
+    ];
+
+    lua = maybe "lua" (with pkgs; [ lua-language-server ]);
+
+    markdown = maybe "markdown" (with pkgs; [
+      python313Packages.pylatexenc
+      quarto
+      zk
+    ]);
+
+    nix = maybe "nix" (with pkgs; [
+      alejandra
+      nix-doc
+      nixd
+    ]);
+
+    optional = maybe "optional" (with pkgs; [
+      bat
+      broot
+      devenv
+      dust
+      fd
+      fzf
+      gawk
+      gh
+      git
+      hunspell
+      hunspellDicts.de-at
+      hunspellDicts.en-us
+      ispell
+      jq
+      just
+      lazygit
+      man
+      ncdu
+      pigz
+      poppler
+      ripgrep
+      tokei
+      wget
+      yq
+      zathura
+    ]);
+
+    python = maybe "python" (let
+      python_packages_fn =
+        if pkgs ? basePythonPackages
+        then ps: pkgs.basePythonPackages ps ++ config.settings.lang_packages.python
+        else _: config.settings.lang_packages.python;
+      python_with_packages = pkgs.python3.withPackages python_packages_fn;
+    in
+      with pkgs; [
+        python_with_packages
+        nodejs
+        ruff
+        basedpyright
+        uv
+      ]);
+
+    r = maybe "r" (let
+      r_packages = (pkgs.baseRPackages or [ ]) ++ config.settings.lang_packages.r;
+    in
+      with pkgs; [
+        (rWrapper.override { packages = r_packages; })
+        radianWrapper
+        (quarto.override { extraRPackages = r_packages; })
+        air-formatter
+        yaml-language-server
+        rnvimserver
+      ]);
+
+    # cats without packages get empty lists
+    general = [ ];
+    gitPlugins = [ ];
+    treesitterParsers = [ pkgs.tree-sitter ];
+    utils = [ ];
+  };
+}
diff --git a/modules/module/settings/cats.nix b/modules/module/settings/cats.nix
index 13758d4..e1895f7 100644
--- a/modules/module/settings/cats.nix
+++ b/modules/module/settings/cats.nix
@@ -13,6 +13,7 @@
       Set a category to `false` to skip its dependency/plugin specs.
 
       Available categories:
+      - always: always-on packages (not gated by a toggle)
       - clickhouse: Clickhouse client and tools
       - external: external tools and integrations
       - general: core Neovim plugins/features
@@ -30,6 +31,7 @@
   };
 
   config.cats = {
+    always = lib.mkDefault true;
     clickhouse = lib.mkDefault false;
     external = lib.mkDefault true;
     general = lib.mkDefault true;
diff --git a/modules/module/settings/runtime-path.nix b/modules/module/settings/runtime-path.nix
deleted file mode 100644
index b321019..0000000
--- a/modules/module/settings/runtime-path.nix
+++ /dev/null
@@ -1,33 +0,0 @@
-{
-  config,
-  lib,
-  ...
-}:
-let
-  collect_runtime_packages = runtime_deps_type:
-    config.specCollect
-      (acc: spec:
-        let
-          is_enabled = if spec ? enable then spec.enable else true;
-          has_runtime_deps = (spec.runtimeDeps or false) == runtime_deps_type;
-          packages = spec.runtimePackages or [ ];
-        in
-        acc ++ lib.optionals (is_enabled && has_runtime_deps) packages
-      )
-      [ ];
-
-  prefix_packages = collect_runtime_packages "prefix";
-
-  to_path_specs = packages: [
-    {
-      data = [
-        "PATH"
-        ":"
-        "${lib.makeBinPath packages}"
-      ];
-    }
-  ];
-in
-{
-  config.prefixVar = lib.optionals (prefix_packages != [ ]) (to_path_specs prefix_packages);
-}
diff --git a/modules/module/specs/deps.nix b/modules/module/specs/deps.nix
index c3a40ea..b0c437f 100644
--- a/modules/module/specs/deps.nix
+++ b/modules/module/specs/deps.nix
@@ -13,133 +13,69 @@
     };
   };
 
-  config.specs.external = {
+  config.specs.always = lib.mkIf (config.cats.always or true) {
+    data = lib.mkDefault null;
+    runtimeDeps = "prefix";
+    runtimePkgs = config.catPkgs.always;
+  };
+
+  config.specs.external = lib.mkIf (config.cats.external or true) {
     data = lib.mkDefault null;
     before = ["INIT_MAIN"];
     config = ''
       vim.o.shell = "${pkgs.zsh}/bin/zsh"
     '';
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
-      perl
-      ruby
-      shfmt
-      sqlfluff
-      tree-sitter
-    ];
+    runtimePkgs = config.catPkgs.external;
   };
 
   config.specs.optional = lib.mkIf (config.cats.optional or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     before = ["INIT_MAIN"];
-    runtimePkgs = with pkgs; [
-      bat
-      broot
-      devenv
-      dust
-      fd
-      fzf
-      gawk
-      gh
-      git
-      hunspell
-      hunspellDicts.de-at
-      hunspellDicts.en-us
-      ispell
-      jq
-      just
-      lazygit
-      man
-      ncdu
-      pigz
-      poppler
-      ripgrep
-      tokei
-      wget
-      yq
-      zathura
-    ];
+    runtimePkgs = config.catPkgs.optional;
   };
 
   config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
-      python313Packages.pylatexenc
-      quarto
-      zk
-    ];
+    runtimePkgs = config.catPkgs.markdown;
   };
 
   config.specs.nix = lib.mkIf (config.cats.nix or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
-      alejandra
-      nix-doc
-      nixd
-    ];
+    runtimePkgs = config.catPkgs.nix;
   };
 
   config.specs.lua = lib.mkIf (config.cats.lua or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
-      lua-language-server
-    ];
+    runtimePkgs = config.catPkgs.lua;
   };
 
   config.specs.python = lib.mkIf (config.cats.python or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = let
-      python_packages_fn =
-        if pkgs ? basePythonPackages
-        then ps: pkgs.basePythonPackages ps ++ config.settings.lang_packages.python
-        else _: config.settings.lang_packages.python;
-      python_with_packages = pkgs.python3.withPackages python_packages_fn;
-    in
-      with pkgs; [
-        python_with_packages
-        nodejs
-        ruff
-        basedpyright
-        uv
-      ];
+    runtimePkgs = config.catPkgs.python;
   };
 
   config.specs.r = lib.mkIf (config.cats.r or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = let
-      r_packages = (pkgs.baseRPackages or []) ++ config.settings.lang_packages.r;
-    in
-      with pkgs; [
-        (rWrapper.override {packages = r_packages;})
-        radianWrapper
-        (quarto.override {extraRPackages = r_packages;})
-        air-formatter
-        yaml-language-server
-        updateR
-      ];
+    runtimePkgs = config.catPkgs.r;
   };
 
   config.specs.julia = lib.mkIf (config.cats.julia or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = let
-      julia_with_packages =
-        pkgs.julia-bin.withPackages config.settings.lang_packages.julia;
-    in [julia_with_packages];
+    runtimePkgs = config.catPkgs.julia;
   };
 
   config.specs.clickhouse = lib.mkIf (config.cats.clickhouse or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
-      clickhouse-lts
-    ];
+    runtimePkgs = config.catPkgs.clickhouse;
   };
 
   config.runtimePkgs = config.specCollect (acc: v: acc ++ (v.runtimePkgs or [])) [];
diff --git a/modules/neovim.nix b/modules/neovim.nix
index 64d2cda..f4ca40f 100644
--- a/modules/neovim.nix
+++ b/modules/neovim.nix
@@ -9,6 +9,7 @@ inputs:
 {
   imports = [
     wlib.wrapperModules.neovim
+    ./module/settings/cat-packages.nix
     ./module/specs/deps.nix
     ./module/specs/plugins.nix
     ./module/settings/core.nix
@@ -16,7 +17,6 @@ inputs:
     ./module/settings/env.nix
     ./module/settings/hosts.nix
     ./module/settings/lang-packages.nix
-    ./module/settings/runtime-path.nix
   ];
 
   options.nvim-lib.neovimPlugins = lib.mkOption {

From db610620b3a3f4a1b4976f466486393cd76f35b2 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sat, 23 May 2026 21:59:54 +1000
Subject: [PATCH 03/11] large refactor

---
 README.md                                 | 158 +++++++++++++++-----
 flake.nix                                 | 167 +++++++++++++---------
 modules/module/settings/cat-packages.nix  |  18 ++-
 modules/module/settings/core.nix          |   2 +-
 modules/module/settings/env.nix           |  10 +-
 modules/module/settings/hosts.nix         |   6 +-
 modules/module/settings/lang-packages.nix |  26 +++-
 modules/module/specs/deps.nix             |  20 +--
 modules/module/specs/plugins.nix          |  20 +--
 plugin/21_datascience.lua                 |   2 +-
 10 files changed, 286 insertions(+), 143 deletions(-)

diff --git a/README.md b/README.md
index c50d03e..cec155c 100644
--- a/README.md
+++ b/README.md
@@ -33,11 +33,9 @@ Modular Neovim wrapper config. Defines a wrapped `vv` binary with per-category p
         config.allowUnfree = true;
         overlays = [ nvimConfig.overlays.dependencies ];
       };
-      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
-        modules = [
-          nvimConfig.wrapperModules.default
-          projectSettings  # see below
-        ];
+      evalResult = nvimConfig.lib.eval {
+        inherit pkgs;
+        modules = [ projectSettings ];  # see below
       };
     in {
       default = evalResult.config.wrap { inherit pkgs; };
@@ -49,19 +47,14 @@ Modular Neovim wrapper config. Defines a wrapped `vv` binary with per-category p
         config.allowUnfree = true;
         overlays = [ nvimConfig.overlays.dependencies ];
       };
-      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
-        modules = [
-          nvimConfig.wrapperModules.default
-          projectSettings
-        ];
+      evalResult = nvimConfig.lib.eval {
+        inherit pkgs;
+        modules = [ projectSettings ];
       };
       nv = evalResult.config.wrap { inherit pkgs; };
     in {
       default = pkgs.mkShell {
-        packages =
-          [ nv ]
-          ++ (evalResult.config.catPkgs.markdown or [])
-          ++ (evalResult.config.catPkgs.nix or []);
+        packages = [ nv ] ++ nvimConfig.lib.devShellPackages evalResult.config;
       };
     });
   };
@@ -92,7 +85,96 @@ Modular Neovim wrapper config. Defines a wrapped `vv` binary with per-category p
 
 ## Overriding settings
 
-Define a `projectSettings` attrset and pass it as the second module in `evalModules`. Every option in `nvimConfig.wrapperConfigs.default` can be overridden here.
+Define a `projectSettings` attrset and pass it to `nvimConfig.lib.eval` or `nvimConfig.lib.mkWrapper`. The helper injects your overlaid `pkgs` automatically, so downstream consumers do not need to wire `specialArgs` themselves. Every option in `nvimConfig.wrapperConfigs.default` can be overridden here. Local `packages.default`, local `devShells.default`, downstream helper usage, and `pkgs.vv` all resolve the same module defaults unless you override them.
+
+### Basic downstream flake example
+
+This example enables a few cats, adds runtime tools to the shared wrapper/devShell package set, and appends language libraries to the default Python and R environments.
+
+```nix
+{
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+    rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
+    fran = {
+      url = "github:dwinkler1/fran";
+      inputs.nixpkgs.follows = "rixpkgs";
+    };
+    nvimConfig = {
+      url = "github:dwinkler1/nvimConfig";
+      inputs = {
+        nixpkgs.follows = "nixpkgs";
+        rixpkgs.follows = "rixpkgs";
+        fran.follows = "fran";
+      };
+    };
+  };
+
+  outputs = { nixpkgs, nvimConfig, ... }: let
+    system = "aarch64-darwin";
+    pkgs = import nixpkgs {
+      inherit system;
+      config.allowUnfree = true;
+      overlays = [ nvimConfig.overlays.dependencies ];
+    };
+    projectSettings = {
+      cats = {
+        python = true;
+        r = true;
+        nix = true;
+        markdown = true;
+        optional = true;
+      };
+
+      settings.lang_packages = {
+        python = with pkgs.python3Packages; [
+          pandas
+          pyarrow
+        ];
+        r = with pkgs.rpkgs.rPackages; [
+          fixest
+          modelsummary
+        ];
+      };
+
+      catPkgs = {
+        python = [
+          (pkgs.python3.withPackages (ps:
+            ps
+            ++ (with ps; [
+              pandas
+              pyarrow
+            ])))
+          pkgs.ruff
+          pkgs.basedpyright
+          pkgs.uv
+          pkgs.nodejs
+        ];
+        nix = [
+          pkgs.alejandra
+          pkgs.nil
+        ];
+        optional = [
+          pkgs.git
+          pkgs.fd
+          pkgs.ripgrep
+        ];
+      };
+    };
+    evalResult = nvimConfig.lib.eval {
+      inherit pkgs;
+      modules = [ projectSettings ];
+    };
+    nv = evalResult.config.wrap { inherit pkgs; };
+  in {
+    packages.${system}.default = nv;
+
+    devShells.${system}.default = pkgs.mkShell {
+      packages = [ nv ] ++ nvimConfig.lib.devShellPackages evalResult.config;
+    };
+  };
+}
+```
 
 ### Categories
 
@@ -112,9 +194,13 @@ projectSettings = {
 };
 ```
 
-### Language packages (overlay extension)
+### Language packages (module defaults)
 
-Add Python/R/Julia libraries that get appended to the overlay base packages.
+Add Python/R/Julia libraries that get appended to the module defaults. The built-in defaults are:
+
+- Python: `duckdb`, `polars`
+- R: `arrow`, `broom`, `data_table`, `janitor`, `styler`, `nvimcom`
+- Julia: `DataFramesMeta`, `QuackIO`
 
 ```nix
 projectSettings = {
@@ -138,7 +224,7 @@ projectSettings = {
 
 ### Runtime dependencies (per-cat packages)
 
-Override `catPkgs` to add tools that appear in both the wrapper PATH and the devShell. To add always-available packages not gated by any cat, use `runtimePkgs` directly (see next section).
+Override `catPkgs` to change the full runtime tool lists that appear in both the wrapper PATH and the devShell. Use normal assignments to merge list values, or `lib.mkForce` to replace them.
 
 ```nix
 projectSettings = {
@@ -179,6 +265,14 @@ projectSettings = {
 
 `env` values are forced; `envDefault` values can be overridden by the user's shell.
 
+### Choosing the right override surface
+
+- Use `cats` to enable or disable a whole language or tooling category.
+- Use `settings.lang_packages` to add or replace Python, R, or Julia libraries within a language environment.
+- Use `catPkgs` to change the full runtime tool list for a category. `config.runtimePkgs` drives wrapper PATH composition, while `nvimConfig.lib.devShellPackages config` returns the package-only list suitable for `mkShell`.
+- Use `env` or `envDefault` for wrapper environment variables.
+- Use `specs` for plugin additions or custom runtime behavior.
+
 ### Neovim settings
 
 ```nix
@@ -226,22 +320,20 @@ projectSettings = {
 ## Architecture
 
 ```
-langPackages (flake.nix) ──► settings.lang_packages (module option)
-                                        │
-cats.nix ──► config.cats                │
-                  │                     │
-                  ▼                     ▼
-          cat-packages.nix ──► config.catPkgs.<cat>
-                  │                     │
-          ┌───────┘                     │
-          ▼                             ▼
-   deps.nix (runtimePkgs)       flake.nix (devShells)
-          │                             │
-          ▼                             ▼
-   wrapped vv PATH              nix develop PATH
+settings/lang-packages.nix ──► settings.lang_packages
+                                             │
+cats.nix ───────────────► config.cats        │
+                     │                       │
+                     ▼                       ▼
+             cat-packages.nix ───────► config.catPkgs.<cat>
+                     │                       │
+                     ├──────────────┐        │
+                     ▼              ▼        ▼
+             deps.nix PATH     wrapper.config.wrap   devShells.default
 ```
 
-- **Overlays** (`overlays/`) inject base packages into nixpkgs (rWrapper, quarto, baseRPackages, basePythonPackages).
+- **Overlays** (`overlays/`) inject dependency package sets into nixpkgs (`rpkgs`, `baseRPackages`, `basePythonPackages`, plugins). Top-level `rWrapper` and `quarto` are compatibility conveniences, but `pkgs.rpkgs` is the canonical R surface for downstream configuration.
 - **cat-packages.nix** is the single source of truth for per-category packages. Each list is gated by its cat toggle.
 - **deps.nix** wires `catPkgs` into the wrapper's runtime PATH.
-- **flake.nix** reads `catPkgs` for the devShell. `langPackages` feeds into `settings.lang_packages`.
+- **settings.lang_packages** holds the shared defaults used by local outputs and downstream module consumers.
+- **flake.nix** exports `lib.eval`, `lib.mkWrapper`, and `lib.devShellPackages` as the canonical downstream helpers, and builds `packages.default` and `devShells.default` from the same module config.
diff --git a/flake.nix b/flake.nix
index cde55df..b9e77e3 100644
--- a/flake.nix
+++ b/flake.nix
@@ -42,40 +42,42 @@
     wrappers,
     ...
   } @ inputs: let
-    langPackages = pkgs: {
-      python = with pkgs.python3Packages; [
-        duckdb
-        polars
-      ];
-      r =
-        (with pkgs.rpkgs.rPackages; [
-          arrow
-          broom
-          data_table
-          janitor
-          styler
-        ])
-        ++ [pkgs.nvimcom];
-      julia = [
-        "DataFramesMeta"
-        "QuackIO"
-      ];
-    };
-
-    mkWrapperConfig = pkgs: {
-      settings = {
-        lang_packages = langPackages pkgs;
-      };
-      binName = "vv";
-    };
-
-    wrapperSettings = pkgs: let
-      cfg = mkWrapperConfig pkgs;
-    in
-      wrapper.config.wrap {
-        inherit pkgs;
-        inherit (cfg) settings binName;
+    devShellCatOrder = [
+      "always"
+      "clickhouse"
+      "external"
+      "julia"
+      "lua"
+      "markdown"
+      "nix"
+      "optional"
+      "python"
+      "r"
+      "treesitterParsers"
+    ];
+    evalWithPkgs = pkgs: extraModules:
+      wrappers.lib.evalModules {
+        specialArgs = {
+          inherit pkgs;
+        };
+        modules =
+          [
+            module
+          ]
+          ++ extraModules;
       };
+    mkDevShellPackages = config:
+      builtins.concatLists (map (name: config.catPkgs.${name} or []) devShellCatOrder);
+    mkShellHook = config:
+      ''
+        echo 'I am a NixShell'
+      ''
+      + nixpkgs.lib.optionalString (config.cats.r or false) ''
+        export R_HOME=$(R RHOME)
+        export R_LIBS_SITE=$(strings "$(command -v R)" | grep -oP '/nix/store/[^:]+/library' | sort -u | paste -sd: -)
+        export R_LIBS_USER="$PWD/.r-libs"
+        mkdir -p "$R_LIBS_USER"
+      '';
 
     systems = [
       "aarch64-darwin"
@@ -93,35 +95,40 @@
         config = {allowUnfree = true;};
         overlays = [
           overlayDefs.dependencyOverlay
-          inputs.r-nvim-nix.overlays.default
-          inputs.fran.overlays.default
         ];
       };
 
     module = (import ./modules/neovim.nix) inputs;
-    wrapper = wrappers.lib.evalModule module;
   in {
+    lib = {
+      eval = {pkgs, modules ? []}: evalWithPkgs pkgs modules;
+      mkWrapper = {pkgs, modules ? []}: (evalWithPkgs pkgs modules).config.wrap {inherit pkgs;};
+      devShellPackages = config: mkDevShellPackages config;
+    };
+
     overlays = {
       # overlay `vv` wraps the module with default settings only.
-      # For the fully-configured binary (including mkWrapperConfig overrides),
-      # use `packages.<system>.default` instead.
+      # It is evaluated against the final package set so module defaults can
+      # depend on overlays such as rixpkgs-backed `pkgs.rpkgs`.
       default = nixpkgs.lib.composeManyExtensions [
         overlayDefs.dependencyOverlay
         (final: prev: {
-          vv = wrapper.config.wrap {pkgs = final;};
+          vv = (evalWithPkgs final []).config.wrap {pkgs = final;};
         })
       ];
       dependencies = overlayDefs.dependencyOverlay;
     };
 
     wrapperModules.default = module;
-    wrapperConfigs.default = wrapper.config;
+    wrapperConfigs.default = {pkgs, modules ? []}: (self.lib.eval {inherit pkgs modules;}).config;
 
     packages = forAllSystems (
       system: let
         pkgs = mkPkgs system;
       in {
-        default = wrapperSettings pkgs;
+        default = self.lib.mkWrapper {
+          inherit pkgs;
+        };
       }
     );
 
@@ -135,30 +142,13 @@
     devShells = forAllSystems (
       system: let
         pkgs = mkPkgs system;
-        nvimPkg = wrapperSettings pkgs;
-
-        shellPackages = [nvimPkg]
-          ++ wrapper.config.catPkgs.always or []
-          ++ wrapper.config.catPkgs.python or []
-          ++ wrapper.config.catPkgs.r or []
-          ++ wrapper.config.catPkgs.julia or []
-          ++ wrapper.config.catPkgs.markdown or []
-          ++ wrapper.config.catPkgs.optional or []
-          ++ wrapper.config.catPkgs.external or []
-          ++ wrapper.config.catPkgs.nix or []
-          ++ wrapper.config.catPkgs.lua or []
-          ++ wrapper.config.catPkgs.clickhouse or [];
+        config = (self.lib.eval {inherit pkgs;}).config;
+        nvimPkg = config.wrap {inherit pkgs;};
       in {
         default = pkgs.mkShell {
           name = "vShell";
-          packages = shellPackages;
-          shellHook = ''
-            echo 'I am a NixShell'
-            export R_HOME=$(R RHOME)
-            export R_LIBS_SITE=$(strings "$(command -v R)" | grep -oP '/nix/store/[^:]+/library' | sort -u | paste -sd: -)
-            export R_LIBS_USER="$PWD/.r-libs"
-            mkdir -p "$R_LIBS_USER"
-          '';
+          packages = [nvimPkg] ++ self.lib.devShellPackages config;
+          shellHook = mkShellHook config;
         };
       }
     );
@@ -166,10 +156,31 @@
     checks = forAllSystems (
       system: let
         pkgs = mkPkgs system;
-        nvimPkg = wrapperSettings pkgs;
+        defaultConfig = (self.lib.eval {inherit pkgs;}).config;
+        defaultNvimPkg = defaultConfig.wrap {inherit pkgs;};
+        defaultShellHook = mkShellHook defaultConfig;
+        overrideConfig =
+          (self.lib.eval {
+            inherit pkgs;
+            modules = [
+              {
+                cats = {
+                  r = false;
+                  python = true;
+                };
+                settings.lang_packages.python = nixpkgs.lib.mkForce (with pkgs.python3Packages; [
+                  pandas
+                ]);
+                catPkgs.nix = nixpkgs.lib.mkForce [
+                  pkgs.alejandra
+                ];
+              }
+            ];
+          }).config;
+        overrideShellHook = mkShellHook overrideConfig;
       in {
         default = pkgs.runCommand "check-vv" {} ''
-          BINARY_PATH="${nvimPkg}/bin/vv"
+          BINARY_PATH="${defaultNvimPkg}/bin/vv"
 
           if [ ! -x "$BINARY_PATH" ]; then
             echo "Error: Binary not found or not executable"
@@ -186,11 +197,37 @@
           fi
         '';
         module-eval = let
-          _ = wrapper.config;
+          _ = (self.lib.eval {inherit pkgs;}).config;
         in
           pkgs.runCommand "check-module-eval" {} ''
             echo "Module evaluation successful" > $out
           '';
+        downstream-overrides = let
+          overrideNix = builtins.map (p: p.pname or p.name) overrideConfig.catPkgs.nix;
+          defaultAssertions = [
+            (defaultConfig.cats.r or false)
+            (builtins.match ".*R RHOME.*" defaultShellHook != null)
+            (builtins.length (self.lib.devShellPackages defaultConfig) > 0)
+          ];
+          overrideAssertions = [
+            (!(overrideConfig.cats.r or false))
+            (builtins.length overrideNix == 1)
+            ((builtins.head overrideNix) == "alejandra")
+            (builtins.match ".*R RHOME.*" overrideShellHook == null)
+          ];
+        in
+          pkgs.runCommand "check-downstream-overrides" {
+            pass =
+              if builtins.all (x: x) (defaultAssertions ++ overrideAssertions)
+              then "1"
+              else "";
+          } ''
+            if [ -z "$pass" ]; then
+              echo "Downstream override assertions failed" >&2
+              exit 1
+            fi
+            echo "Downstream override assertions passed" > $out
+          '';
       }
     );
 
diff --git a/modules/module/settings/cat-packages.nix b/modules/module/settings/cat-packages.nix
index 3570ff6..7dd3049 100644
--- a/modules/module/settings/cat-packages.nix
+++ b/modules/module/settings/cat-packages.nix
@@ -70,7 +70,6 @@ in
       tokei
       wget
       yq
-      zathura
     ]);
 
     python = maybe "python" (let
@@ -90,15 +89,14 @@ in
 
     r = maybe "r" (let
       r_packages = (pkgs.baseRPackages or [ ]) ++ config.settings.lang_packages.r;
-    in
-      with pkgs; [
-        (rWrapper.override { packages = r_packages; })
-        radianWrapper
-        (quarto.override { extraRPackages = r_packages; })
-        air-formatter
-        yaml-language-server
-        rnvimserver
-      ]);
+    in [
+      (pkgs.rpkgs.rWrapper.override { packages = r_packages; })
+      pkgs.rpkgs.radianWrapper
+      (pkgs.rpkgs.quarto.override { extraRPackages = r_packages; })
+      pkgs.air-formatter
+      pkgs.yaml-language-server
+      pkgs.rnvimserver
+    ]);
 
     # cats without packages get empty lists
     general = [ ];
diff --git a/modules/module/settings/core.nix b/modules/module/settings/core.nix
index ec9bb5c..f8b3188 100644
--- a/modules/module/settings/core.nix
+++ b/modules/module/settings/core.nix
@@ -16,7 +16,7 @@
 
   # Lua packages available to neovim (for :lua require())
   config.settings.nvim_lua_env = lp:
-    lib.optionals (config.cats.general or true) [ lp.tiktoken_core ];
+    lib.optionals (config.cats.general or false) [ lp.tiktoken_core ];
 
   # Binary name for the wrapper
   config.binName = lib.mkDefault "vv";
diff --git a/modules/module/settings/env.nix b/modules/module/settings/env.nix
index 2fcab8a..db2986d 100644
--- a/modules/module/settings/env.nix
+++ b/modules/module/settings/env.nix
@@ -7,21 +7,21 @@
   # Environment variables set for the wrapper.
   # These are available when running neovim.
   config.env = lib.mkMerge [
-    (lib.mkIf (config.cats.python or true) {
+    (lib.mkIf (config.cats.python or false) {
       UV_PYTHON_DOWNLOADS = "never";
       UV_PYTHON = pkgs.python.interpreter;
     })
-    (lib.mkIf (config.cats.r or true) {
+    (lib.mkIf (config.cats.r or false) {
       RNVIM_COMPLDIR = "$PWD/.r-compl";
-      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
+      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.r-libs";
       TMPDIR = "$PWD/.r-tmp";
     })
   ];
 
   # Environment variables with defaults (can be overridden by user)
   config.envDefault = lib.mkMerge [
-    (lib.mkIf (config.cats.r or true) {
-      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
+    (lib.mkIf (config.cats.r or false) {
+      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.r-libs";
     })
   ];
 }
diff --git a/modules/module/settings/hosts.nix b/modules/module/settings/hosts.nix
index f248a00..7637633 100644
--- a/modules/module/settings/hosts.nix
+++ b/modules/module/settings/hosts.nix
@@ -29,7 +29,7 @@
         ];
       };
     }
-    (lib.mkIf (config.cats.julia or true) {
+    (lib.mkIf (config.cats.julia or false) {
       jl = {
         nvim-host.enable = true;
         nvim-host.package = "${pkgs.julia-bin}/bin/julia";
@@ -39,10 +39,10 @@
         ];
       };
     })
-    (lib.mkIf (config.cats.python or true) {
+    (lib.mkIf (config.cats.python or false) {
       python3.nvim-host.enable = true;
     })
-    (lib.mkIf (config.cats.r or true) {
+    (lib.mkIf (config.cats.r or false) {
       r = {
         nvim-host.enable = true;
         nvim-host.package = "${pkgs.rWrapper}/bin/R";
diff --git a/modules/module/settings/lang-packages.nix b/modules/module/settings/lang-packages.nix
index 531b811..b6fff27 100644
--- a/modules/module/settings/lang-packages.nix
+++ b/modules/module/settings/lang-packages.nix
@@ -1,5 +1,6 @@
 {
   config,
+  pkgs,
   lib,
   ...
 }:
@@ -26,14 +27,29 @@
     };
     default = { };
     description = ''
-      Language-specific package overrides appended to each language spec's runtimePackages.
-      Intended for flake.nix overrides via wrapper.config.wrap.
+      Language-specific package defaults and downstream overrides appended to each
+      language spec's runtime packages.
     '';
   };
 
   config.settings.lang_packages = {
-    python = lib.mkDefault [ ];
-    r = lib.mkDefault [ ];
-    julia = lib.mkDefault [ ];
+    python = lib.mkDefault (with pkgs.python3Packages; [
+      duckdb
+      polars
+    ]);
+    r = lib.mkDefault (
+      (with pkgs.rpkgs.rPackages; [
+        arrow
+        broom
+        data_table
+        janitor
+        styler
+      ])
+      ++ [pkgs.nvimcom]
+    );
+    julia = lib.mkDefault [
+      "DataFramesMeta"
+      "QuackIO"
+    ];
   };
 }
diff --git a/modules/module/specs/deps.nix b/modules/module/specs/deps.nix
index b0c437f..5cbfe63 100644
--- a/modules/module/specs/deps.nix
+++ b/modules/module/specs/deps.nix
@@ -13,13 +13,13 @@
     };
   };
 
-  config.specs.always = lib.mkIf (config.cats.always or true) {
+  config.specs.always = lib.mkIf (config.cats.always or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.always;
   };
 
-  config.specs.external = lib.mkIf (config.cats.external or true) {
+  config.specs.external = lib.mkIf (config.cats.external or false) {
     data = lib.mkDefault null;
     before = ["INIT_MAIN"];
     config = ''
@@ -29,50 +29,50 @@
     runtimePkgs = config.catPkgs.external;
   };
 
-  config.specs.optional = lib.mkIf (config.cats.optional or true) {
+  config.specs.optional = lib.mkIf (config.cats.optional or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     before = ["INIT_MAIN"];
     runtimePkgs = config.catPkgs.optional;
   };
 
-  config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
+  config.specs.markdown = lib.mkIf (config.cats.markdown or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.markdown;
   };
 
-  config.specs.nix = lib.mkIf (config.cats.nix or true) {
+  config.specs.nix = lib.mkIf (config.cats.nix or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.nix;
   };
 
-  config.specs.lua = lib.mkIf (config.cats.lua or true) {
+  config.specs.lua = lib.mkIf (config.cats.lua or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.lua;
   };
 
-  config.specs.python = lib.mkIf (config.cats.python or true) {
+  config.specs.python = lib.mkIf (config.cats.python or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.python;
   };
 
-  config.specs.r = lib.mkIf (config.cats.r or true) {
+  config.specs.r = lib.mkIf (config.cats.r or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.r;
   };
 
-  config.specs.julia = lib.mkIf (config.cats.julia or true) {
+  config.specs.julia = lib.mkIf (config.cats.julia or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.julia;
   };
 
-  config.specs.clickhouse = lib.mkIf (config.cats.clickhouse or true) {
+  config.specs.clickhouse = lib.mkIf (config.cats.clickhouse or false) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     runtimePkgs = config.catPkgs.clickhouse;
diff --git a/modules/module/specs/plugins.nix b/modules/module/specs/plugins.nix
index ff00a72..ad464b8 100644
--- a/modules/module/specs/plugins.nix
+++ b/modules/module/specs/plugins.nix
@@ -4,11 +4,11 @@
   lib,
   ...
 }: {
-  config.specs.gitPlugins = lib.mkIf (config.cats.gitPlugins or true) {
+  config.specs.gitPlugins = lib.mkIf (config.cats.gitPlugins or false) {
     data = [];
   };
 
-  config.specs.r = lib.mkIf (config.cats.r or true) {
+  config.specs.r = lib.mkIf (config.cats.r or false) {
     data = with pkgs.vimPlugins; [
       pkgs.r-nvim
       quarto-nvim
@@ -19,14 +19,14 @@
     ];
   };
 
-  config.specs.markdown-lazy = lib.mkIf (config.cats.markdown or true) {
+  config.specs.markdown-lazy = lib.mkIf (config.cats.markdown or false) {
     lazy = true;
     data = [
       config.nvim-lib.neovimPlugins.cmp-pandoc-references
     ];
   };
 
-  config.specs.general = lib.mkIf (config.cats.general or true) {
+  config.specs.general = lib.mkIf (config.cats.general or false) {
     data = with pkgs.vimPlugins; [
       lze
       lzextras
@@ -79,7 +79,7 @@
     ];
   };
 
-  config.specs.lua = lib.mkIf (config.cats.lua or true) {
+  config.specs.lua = lib.mkIf (config.cats.lua or false) {
     data = with pkgs.vimPlugins; [
       luvit-meta
       {
@@ -89,7 +89,7 @@
     ];
   };
 
-  config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
+  config.specs.markdown = lib.mkIf (config.cats.markdown or false) {
     data = with pkgs.vimPlugins; [
       quarto-nvim
       render-markdown-nvim
@@ -104,7 +104,7 @@
     ];
   };
 
-  config.specs.utils = lib.mkIf (config.cats.utils or true) {
+  config.specs.utils = lib.mkIf (config.cats.utils or false) {
     data = with pkgs.vimPlugins; [
       blink-cmp
       nvim-lspconfig
@@ -119,7 +119,7 @@
     ];
   };
 
-  config.specs.treesitterParsers = lib.mkIf (config.cats.treesitterParsers or true) {
+  config.specs.treesitterParsers = lib.mkIf (config.cats.treesitterParsers or false) {
     data = with pkgs.vimPlugins.nvim-treesitter-parsers; [
       bash
       c
@@ -158,7 +158,7 @@
     ];
   };
 
-  config.specs.utils-lazy = lib.mkIf (config.cats.utils or true) {
+  config.specs.utils-lazy = lib.mkIf (config.cats.utils or false) {
     lazy = true;
     data = with pkgs.vimPlugins; [
       blink-compat
@@ -175,7 +175,7 @@
     ];
   };
 
-  config.specs.gitPlugins-lazy = lib.mkIf (config.cats.gitPlugins or true) {
+  config.specs.gitPlugins-lazy = lib.mkIf (config.cats.gitPlugins or false) {
     lazy = true;
     data = [];
   };
diff --git a/plugin/21_datascience.lua b/plugin/21_datascience.lua
index 2e9f86c..aeab360 100644
--- a/plugin/21_datascience.lua
+++ b/plugin/21_datascience.lua
@@ -61,7 +61,7 @@ now(function()
       min_editor_width = 80,
       rconsole_height = 20,
       nvimpager = "split_h",
-      pdfviewer = "zathura",
+      pdfviewer = "",
     })
   end
 end)

From ed7abad63cb63025d5d87a9a767ec5c00d7b3126 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sat, 23 May 2026 22:53:52 +1000
Subject: [PATCH 04/11] Expose shellhooks via API

---
 README.md | 4 +++-
 flake.nix | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index cec155c..715d4c6 100644
--- a/README.md
+++ b/README.md
@@ -55,6 +55,7 @@ Modular Neovim wrapper config. Defines a wrapped `vv` binary with per-category p
     in {
       default = pkgs.mkShell {
         packages = [ nv ] ++ nvimConfig.lib.devShellPackages evalResult.config;
+        shellHook = nvimConfig.lib.shellHook evalResult.config;
       };
     });
   };
@@ -171,6 +172,7 @@ This example enables a few cats, adds runtime tools to the shared wrapper/devShe
 
     devShells.${system}.default = pkgs.mkShell {
       packages = [ nv ] ++ nvimConfig.lib.devShellPackages evalResult.config;
+      shellHook = nvimConfig.lib.shellHook evalResult.config;
     };
   };
 }
@@ -336,4 +338,4 @@ cats.nix ───────────────► config.cats        │
 - **cat-packages.nix** is the single source of truth for per-category packages. Each list is gated by its cat toggle.
 - **deps.nix** wires `catPkgs` into the wrapper's runtime PATH.
 - **settings.lang_packages** holds the shared defaults used by local outputs and downstream module consumers.
-- **flake.nix** exports `lib.eval`, `lib.mkWrapper`, and `lib.devShellPackages` as the canonical downstream helpers, and builds `packages.default` and `devShells.default` from the same module config.
+- **flake.nix** exports `lib.eval`, `lib.mkWrapper`, `lib.devShellPackages`, and `lib.shellHook` as the canonical downstream helpers, and builds `packages.default` and `devShells.default` from the same module config.
diff --git a/flake.nix b/flake.nix
index b9e77e3..4c8df73 100644
--- a/flake.nix
+++ b/flake.nix
@@ -104,6 +104,7 @@
       eval = {pkgs, modules ? []}: evalWithPkgs pkgs modules;
       mkWrapper = {pkgs, modules ? []}: (evalWithPkgs pkgs modules).config.wrap {inherit pkgs;};
       devShellPackages = config: mkDevShellPackages config;
+      shellHook = config: mkShellHook config;
     };
 
     overlays = {

From 1c5619312db77493cc07fd5ac991347e47638e5f Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sat, 23 May 2026 23:07:54 +1000
Subject: [PATCH 05/11] simplified

---
 flake.lock          | 18 ------------------
 flake.nix           |  5 -----
 overlays/r.nix      |  1 -
 scripts/updater.nix | 14 --------------
 scripts/updater.sh  | 22 ----------------------
 5 files changed, 60 deletions(-)
 delete mode 100644 scripts/updater.nix
 delete mode 100644 scripts/updater.sh

diff --git a/flake.lock b/flake.lock
index 02745a6..0b89d7a 100644
--- a/flake.lock
+++ b/flake.lock
@@ -52,23 +52,6 @@
         "type": "github"
       }
     },
-    "plugins-r": {
-      "flake": false,
-      "locked": {
-        "lastModified": 1776905071,
-        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
-        "owner": "R-nvim",
-        "repo": "R.nvim",
-        "rev": "582f2af11290ac067e49018db38e12a511325556",
-        "type": "github"
-      },
-      "original": {
-        "owner": "R-nvim",
-        "ref": "v0.99.4",
-        "repo": "R.nvim",
-        "type": "github"
-      }
-    },
     "r-nvim-nix": {
       "inputs": {
         "nixpkgs": [
@@ -129,7 +112,6 @@
         "fran": "fran",
         "nixpkgs": "nixpkgs",
         "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
-        "plugins-r": "plugins-r",
         "r-nvim-nix": "r-nvim-nix",
         "rixpkgs": "rixpkgs",
         "wrappers": "wrappers"
diff --git a/flake.nix b/flake.nix
index 4c8df73..ee9c05c 100644
--- a/flake.nix
+++ b/flake.nix
@@ -25,11 +25,6 @@
       };
     };
 
-    "plugins-r" = {
-      url = "github:R-nvim/R.nvim/v0.99.4";
-      flake = false;
-    };
-
     "plugins-cmp-pandoc-references" = {
       url = "github:jmbuhr/cmp-pandoc-references";
       flake = false;
diff --git a/overlays/r.nix b/overlays/r.nix
index 14c02eb..18f01dd 100644
--- a/overlays/r.nix
+++ b/overlays/r.nix
@@ -11,5 +11,4 @@ in {
   baseRPackages = [ ];
   rWrapper = rpkgs.rWrapper.override {packages = [ ];};
   quarto = rpkgs.quarto.override {extraRPackages = [ ];};
-  updateR = import ../scripts/updater.nix {pkgs = final;};
 }
diff --git a/scripts/updater.nix b/scripts/updater.nix
deleted file mode 100644
index 063ec8d..0000000
--- a/scripts/updater.nix
+++ /dev/null
@@ -1,14 +0,0 @@
-{pkgs}:
-pkgs.writeShellApplication {
-  name = "updateR";
-
-  # Tools your script needs at runtime
-  runtimeInputs = [
-    pkgs.wget
-    pkgs.gnused
-    pkgs.coreutils
-  ];
-
-  # Keep script in separate file, but embed contents
-  text = builtins.readFile ./updater.sh;
-}
diff --git a/scripts/updater.sh b/scripts/updater.sh
deleted file mode 100644
index ccf5e2e..0000000
--- a/scripts/updater.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-echo "📡 Fetching latest R version from rstats-on-nix..."
-RVER=$( wget -qO- 'https://raw.githubusercontent.com/ropensci/rix/refs/heads/main/inst/extdata/available_df.csv' | tail -n 1 | head -n 1 | cut -d',' -f4 | tr -d '"' )
-
-# Validate RVER matches YYYY-MM-DD format
-if [[ ! "$RVER" =~ ^[0-9]{4}-[0-9]{2}-[0-9]{2}$ ]]; then
-  echo "❌ Error: Failed to fetch valid R version date. Got: '$RVER'"
-  exit 1
-fi
-
-echo "✅ R date is $RVER"
-
-# Create backup of flake.nix before modifying
-cp flake.nix flake.nix.backup
-
-# Update rixpkgs date in flake.nix
-if sed -i "s|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}\";|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/$RVER\";|" flake.nix; then
-  echo "✅ Updated rixpkgs date in flake.nix"
-  rm flake.nix.backup
-else
-  echo "⚠️  Warning: Failed to update flake.nix, restoring backup"
-  mv flake.nix.backup flake.nix
-fi

From d218b05d485d8d2db387c1d7a6016fdd6f3f1310 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sat, 23 May 2026 23:38:18 +1000
Subject: [PATCH 06/11] hopefully R fix

---
 modules/module/settings/cat-packages.nix | 17 ++++++++++-------
 modules/module/settings/hosts.nix        |  6 +++++-
 2 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/modules/module/settings/cat-packages.nix b/modules/module/settings/cat-packages.nix
index 7dd3049..8f027ba 100644
--- a/modules/module/settings/cat-packages.nix
+++ b/modules/module/settings/cat-packages.nix
@@ -7,6 +7,11 @@
 let
   maybe = cat: pkgsList:
     lib.optionals (config.cats.${cat} or false) pkgsList;
+  rPackages = (pkgs.baseRPackages or [ ]) ++ config.settings.lang_packages.r;
+  quartoPkg =
+    if config.cats.r or false
+    then pkgs.rpkgs.quarto.override { extraRPackages = rPackages; }
+    else pkgs.quarto;
 in
 {
   options.catPkgs = lib.mkOption {
@@ -35,7 +40,7 @@ in
 
     markdown = maybe "markdown" (with pkgs; [
       python313Packages.pylatexenc
-      quarto
+      quartoPkg
       zk
     ]);
 
@@ -87,16 +92,14 @@ in
         uv
       ]);
 
-    r = maybe "r" (let
-      r_packages = (pkgs.baseRPackages or [ ]) ++ config.settings.lang_packages.r;
-    in [
-      (pkgs.rpkgs.rWrapper.override { packages = r_packages; })
+    r = maybe "r" [
+      (pkgs.rpkgs.rWrapper.override { packages = rPackages; })
       pkgs.rpkgs.radianWrapper
-      (pkgs.rpkgs.quarto.override { extraRPackages = r_packages; })
+      quartoPkg
       pkgs.air-formatter
       pkgs.yaml-language-server
       pkgs.rnvimserver
-    ]);
+    ];
 
     # cats without packages get empty lists
     general = [ ];
diff --git a/modules/module/settings/hosts.nix b/modules/module/settings/hosts.nix
index 7637633..a47467a 100644
--- a/modules/module/settings/hosts.nix
+++ b/modules/module/settings/hosts.nix
@@ -4,6 +4,10 @@
   lib,
   ...
 }:
+let
+  rPackages = (pkgs.baseRPackages or [ ]) ++ config.settings.lang_packages.r;
+  rWrapperPkg = pkgs.rpkgs.rWrapper.override { packages = rPackages; };
+in
 {
   config.hosts = lib.mkMerge [
     {
@@ -45,7 +49,7 @@
     (lib.mkIf (config.cats.r or false) {
       r = {
         nvim-host.enable = true;
-        nvim-host.package = "${pkgs.rWrapper}/bin/R";
+        nvim-host.package = "${rWrapperPkg}/bin/R";
         nvim-host.argv0 = "R";
         nvim-host.addFlag = [
           "--no-save"

From 740f86ad7b3494f51e1e051bf709aedcaa0ec11e Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sat, 23 May 2026 23:41:48 +1000
Subject: [PATCH 07/11] hopefully R fix

---
 modules/module/settings/env.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/module/settings/env.nix b/modules/module/settings/env.nix
index db2986d..d7ecc36 100644
--- a/modules/module/settings/env.nix
+++ b/modules/module/settings/env.nix
@@ -13,7 +13,7 @@
     })
     (lib.mkIf (config.cats.r or false) {
       RNVIM_COMPLDIR = "$PWD/.r-compl";
-      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.r-libs";
+      R_LIBS_USER = "$PWD/.r-libs";
       TMPDIR = "$PWD/.r-tmp";
     })
   ];
@@ -21,7 +21,7 @@
   # Environment variables with defaults (can be overridden by user)
   config.envDefault = lib.mkMerge [
     (lib.mkIf (config.cats.r or false) {
-      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.r-libs";
+      R_LIBS_USER = "$PWD/.r-libs";
     })
   ];
 }

From 458332a141840cdad6dc431a8fe9c3f3be5fea94 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sat, 23 May 2026 23:44:56 +1000
Subject: [PATCH 08/11] hopefully R fix

---
 README.md                                 | 2 +-
 modules/module/settings/cat-packages.nix  | 3 ++-
 modules/module/settings/hosts.nix         | 2 +-
 modules/module/settings/lang-packages.nix | 1 -
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 715d4c6..068d704 100644
--- a/README.md
+++ b/README.md
@@ -201,7 +201,7 @@ projectSettings = {
 Add Python/R/Julia libraries that get appended to the module defaults. The built-in defaults are:
 
 - Python: `duckdb`, `polars`
-- R: `arrow`, `broom`, `data_table`, `janitor`, `styler`, `nvimcom`
+- R: `arrow`, `broom`, `data_table`, `janitor`, `styler`
 - Julia: `DataFramesMeta`, `QuackIO`
 
 ```nix
diff --git a/modules/module/settings/cat-packages.nix b/modules/module/settings/cat-packages.nix
index 8f027ba..6406327 100644
--- a/modules/module/settings/cat-packages.nix
+++ b/modules/module/settings/cat-packages.nix
@@ -8,6 +8,7 @@ let
   maybe = cat: pkgsList:
     lib.optionals (config.cats.${cat} or false) pkgsList;
   rPackages = (pkgs.baseRPackages or [ ]) ++ config.settings.lang_packages.r;
+  rWrapperPackages = rPackages ++ [pkgs.nvimcom];
   quartoPkg =
     if config.cats.r or false
     then pkgs.rpkgs.quarto.override { extraRPackages = rPackages; }
@@ -93,7 +94,7 @@ in
       ]);
 
     r = maybe "r" [
-      (pkgs.rpkgs.rWrapper.override { packages = rPackages; })
+      (pkgs.rpkgs.rWrapper.override { packages = rWrapperPackages; })
       pkgs.rpkgs.radianWrapper
       quartoPkg
       pkgs.air-formatter
diff --git a/modules/module/settings/hosts.nix b/modules/module/settings/hosts.nix
index a47467a..aadd70f 100644
--- a/modules/module/settings/hosts.nix
+++ b/modules/module/settings/hosts.nix
@@ -6,7 +6,7 @@
 }:
 let
   rPackages = (pkgs.baseRPackages or [ ]) ++ config.settings.lang_packages.r;
-  rWrapperPkg = pkgs.rpkgs.rWrapper.override { packages = rPackages; };
+  rWrapperPkg = pkgs.rpkgs.rWrapper.override { packages = rPackages ++ [pkgs.nvimcom]; };
 in
 {
   config.hosts = lib.mkMerge [
diff --git a/modules/module/settings/lang-packages.nix b/modules/module/settings/lang-packages.nix
index b6fff27..a91d9a5 100644
--- a/modules/module/settings/lang-packages.nix
+++ b/modules/module/settings/lang-packages.nix
@@ -45,7 +45,6 @@
         janitor
         styler
       ])
-      ++ [pkgs.nvimcom]
     );
     julia = lib.mkDefault [
       "DataFramesMeta"

From 62f456ed46a4c283877bad845af6e404d637284a Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sat, 23 May 2026 23:54:07 +1000
Subject: [PATCH 09/11] hopefully R fix

---
 modules/module/settings/cat-packages.nix | 2 +-
 modules/module/settings/env.nix          | 7 +------
 2 files changed, 2 insertions(+), 7 deletions(-)

diff --git a/modules/module/settings/cat-packages.nix b/modules/module/settings/cat-packages.nix
index 6406327..b92c331 100644
--- a/modules/module/settings/cat-packages.nix
+++ b/modules/module/settings/cat-packages.nix
@@ -8,7 +8,7 @@ let
   maybe = cat: pkgsList:
     lib.optionals (config.cats.${cat} or false) pkgsList;
   rPackages = (pkgs.baseRPackages or [ ]) ++ config.settings.lang_packages.r;
-  rWrapperPackages = rPackages ++ [pkgs.nvimcom];
+  rWrapperPackages = rPackages;
   quartoPkg =
     if config.cats.r or false
     then pkgs.rpkgs.quarto.override { extraRPackages = rPackages; }
diff --git a/modules/module/settings/env.nix b/modules/module/settings/env.nix
index d7ecc36..c7a1a8b 100644
--- a/modules/module/settings/env.nix
+++ b/modules/module/settings/env.nix
@@ -13,15 +13,10 @@
     })
     (lib.mkIf (config.cats.r or false) {
       RNVIM_COMPLDIR = "$PWD/.r-compl";
-      R_LIBS_USER = "$PWD/.r-libs";
       TMPDIR = "$PWD/.r-tmp";
     })
   ];
 
   # Environment variables with defaults (can be overridden by user)
-  config.envDefault = lib.mkMerge [
-    (lib.mkIf (config.cats.r or false) {
-      R_LIBS_USER = "$PWD/.r-libs";
-    })
-  ];
+  config.envDefault = lib.mkMerge [ ];
 }

From aec9110e709e1aa50d78f06293c4bde14974b23f Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sun, 24 May 2026 00:01:12 +1000
Subject: [PATCH 10/11] hopefully R fix

---
 modules/module/settings/core.nix | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/modules/module/settings/core.nix b/modules/module/settings/core.nix
index f8b3188..822fc53 100644
--- a/modules/module/settings/core.nix
+++ b/modules/module/settings/core.nix
@@ -32,4 +32,10 @@
 
   # Enable wrapper handling of spec runtimeDeps (template pattern).
   config.settings.autowrapRuntimeDeps = true;
+
+  # The wrapper library currently emits runtime PATH additions via `suffixVar`,
+  # which lets host-level tools in `/usr/local/bin` win inside `nix run`.
+  # Mirror those additions into `prefixVar` so wrapped Neovim resolves the
+  # Nix-provided toolchain first while preserving existing wrapper behavior.
+  config.prefixVar = lib.mkAfter config.suffixVar;
 }

From d49ad725715a40fe0e490569dac2effc09f734e1 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Sun, 24 May 2026 06:40:39 +0000
Subject: [PATCH 11/11] flake.lock: Update
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Flake lock file updates:

• Updated input 'nixpkgs':
    'github:nixos/nixpkgs/d233902' (2026-05-15)
  → 'github:nixos/nixpkgs/2991645' (2026-05-23)
• Updated input 'wrappers':
    'github:BirdeeHub/nix-wrapper-modules/e7ed7a1' (2026-05-20)
  → 'github:BirdeeHub/nix-wrapper-modules/8c90cbe' (2026-05-23)
---
 flake.lock | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/flake.lock b/flake.lock
index 0b89d7a..45f57c3 100644
--- a/flake.lock
+++ b/flake.lock
@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1778869304,
-        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
+        "lastModified": 1779508470,
+        "narHash": "sha256-Ap9KJX+5xHIn3bPIpfNgT6MEXdAECECwo4/rmlQD74M=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "d233902339c02a9c334e7e593de68855ad26c4cb",
+        "rev": "29916453413845e54a65b8a1cf996842300cd299",
         "type": "github"
       },
       "original": {
@@ -124,11 +124,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1779297405,
-        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
+        "lastModified": 1779512817,
+        "narHash": "sha256-Y2S3mvEezyKL/A4XUkgVbhuvob9YKfnG25NuJDl8fuQ=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
+        "rev": "8c90cbe3aaae094370b08f270682fc352fcbcb91",
         "type": "github"
       },
       "original": {