From e9c99811d4b8684814608c7bff89dd5bb4d20cda Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sun, 3 May 2026 16:35:56 +1000
Subject: [PATCH 01/28] feat(devshell): add language tools conditionally based
 on cats

- Extract mkWrapperConfig to share cats/settings between package and devshell
- Add python, R, julia, and markdown packages to devShells when their cats are enabled
- Reuse same package construction logic as specs/deps.nix for consistency
- Keep lang_packages overridable via lib.mkDefault for downstream flakes
---
 flake.nix | 120 +++++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 88 insertions(+), 32 deletions(-)

diff --git a/flake.nix b/flake.nix
index cce0107..6dc8545 100644
--- a/flake.nix
+++ b/flake.nix
@@ -36,45 +36,58 @@
     wrappers,
     ...
   } @ inputs: let
+    mkWrapperConfig = pkgs: {
+      cats = {
+        clickhouse = false;
+        gitPlugins = true;
+        julia = false;
+        lua = true;
+        markdown = false;
+        nix = true;
+        optional = false;
+        python = false;
+        r = false;
+      };
+      settings = {
+        lang_packages = {
+          python = with pkgs.python3Packages; [
+            duckdb
+            polars
+          ];
+          r = with pkgs.rpkgs.rPackages; [
+            arrow
+            broom
+            data_table
+            janitor
+            styler
+          ];
+          julia = ["DataFramesMeta" "QuackIO"];
+        };
+        colorscheme = "cyberdream";
+        background = "dark";
+        wrapRc = true;
+      };
+      binName = "vv";
+    };
+
     wrapperSettings = pkgs: let
+      cfg = mkWrapperConfig pkgs;
       def = pkgs.lib.mkDefault;
     in
       wrapper.config.wrap {
         inherit pkgs;
-        cats = {
-          clickhouse = def false;
-          gitPlugins = def true;
-          julia = def false;
-          lua = def true;
-          markdown = def false;
-          nix = def true;
-          optional = def false;
-          python = def false;
-          r = def false;
-        };
-
+        cats = pkgs.lib.mapAttrs (_: v: def v) cfg.cats;
         settings = {
           lang_packages = {
-            python = with pkgs.python3Packages; [
-              duckdb
-              polars
-            ];
-
-            r = with pkgs.rpkgs.rPackages; [
-              arrow
-              broom
-              data_table
-              janitor
-              styler
-            ];
-
-            julia = ["DataFramesMeta" "QuackIO"];
+            python = def cfg.settings.lang_packages.python;
+            r = def cfg.settings.lang_packages.r;
+            julia = def cfg.settings.lang_packages.julia;
           };
-          colorscheme = def "cyberdream";
-          background = def "dark";
-          wrapRc = def true;
+          colorscheme = def cfg.settings.colorscheme;
+          background = def cfg.settings.background;
+          wrapRc = def cfg.settings.wrapRc;
         };
-        binName = def "vv";
+        binName = def cfg.binName;
       };
 
     systems = [
@@ -146,12 +159,55 @@
     devShells = forAllSystems (
       system: let
         pkgs = mkPkgs system;
+        cfg = mkWrapperConfig pkgs;
         nvimPkg = wrapperSettings pkgs;
+
+        pythonPackages = let
+          python_packages_fn =
+            if pkgs ? basePythonPackages
+            then ps: pkgs.basePythonPackages ps ++ cfg.settings.lang_packages.python
+            else _: cfg.settings.lang_packages.python;
+        in
+          with pkgs; [
+            (python3.withPackages python_packages_fn)
+            nodejs
+            ruff
+            basedpyright
+            uv
+          ];
+
+        rPackages = let
+          r_packages = (pkgs.baseRPackages or []) ++ cfg.settings.lang_packages.r;
+        in
+          with pkgs; [
+            (rWrapper.override {packages = r_packages;})
+            radianWrapper
+            (quarto.override {extraRPackages = r_packages;})
+            air-formatter
+            yaml-language-server
+            updateR
+          ];
+
+        juliaPackages = let
+          julia_with_packages = pkgs.julia-bin.withPackages cfg.settings.lang_packages.julia;
+        in [julia_with_packages];
+
+        markdownPackages = with pkgs; [
+          python313Packages.pylatexenc
+          quarto
+          zk
+        ];
+
+        shellPackages = [nvimPkg]
+          ++ pkgs.lib.optionals cfg.cats.python pythonPackages
+          ++ pkgs.lib.optionals cfg.cats.r rPackages
+          ++ pkgs.lib.optionals cfg.cats.julia juliaPackages
+          ++ pkgs.lib.optionals cfg.cats.markdown markdownPackages;
       in {
         default = pkgs.mkShell {
           name = "vShell";
-          packages = [nvimPkg];
-          nativeBuildInputs = with pkgs; [] ++ (pkgs.lib.optionals self.wrappers.default.cats.optional [devenv]);
+          packages = shellPackages;
+          nativeBuildInputs = with pkgs; [] ++ (pkgs.lib.optionals cfg.cats.optional [devenv]);
           inputsFrom = [];
           shellHook = "";
         };

From ed24f176bc7bdb3a042d8fbca9a5e9a1fa165209 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sun, 3 May 2026 16:58:11 +1000
Subject: [PATCH 02/28] feat(r): add R languageserver for Neovim LSP

- Add languageserver to settings.lang_packages.r
- Enable r_language_server in LSP config (plugin/25_lsp.lua)
---
 flake.nix         |  1 +
 plugin/25_lsp.lua | 22 +++++++++++-----------
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/flake.nix b/flake.nix
index 6dc8545..f7db07c 100644
--- a/flake.nix
+++ b/flake.nix
@@ -59,6 +59,7 @@
             broom
             data_table
             janitor
+            languageserver
             styler
           ];
           julia = ["DataFramesMeta" "QuackIO"];
diff --git a/plugin/25_lsp.lua b/plugin/25_lsp.lua
index 8c67295..9591da3 100644
--- a/plugin/25_lsp.lua
+++ b/plugin/25_lsp.lua
@@ -15,17 +15,17 @@ now_if_args(function()
     marksman = {
       filetypes = { "markdown", "markdown_inline", "codecompanion" },
     },
-    -- r_language_server = {
-    --   filetypes = { 'r', 'rmd', 'rmarkdown' },
-    --   settings = {
-    --     ['r_language_server'] = {
-    --       lsp = {
-    --         rich_documentation = true,
-    --         enable = true,
-    --       },
-    --     },
-    --   }
-    -- },
+    r_language_server = {
+      filetypes = { 'r', 'rmd', 'rmarkdown' },
+      settings = {
+        ['r_language_server'] = {
+          lsp = {
+            rich_documentation = true,
+            enable = true,
+          },
+        },
+      }
+    },
     julials = {
       settings = {
         julia = {

From 4884bf685f157da4f4d60f8e40febeac0b9bf0e9 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Thu, 7 May 2026 10:48:37 +1000
Subject: [PATCH 03/28] up

---
 flake.lock | 19 ++++++++++---------
 flake.nix  |  2 +-
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/flake.lock b/flake.lock
index 78a5bd8..32a6765 100644
--- a/flake.lock
+++ b/flake.lock
@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1776169885,
-        "narHash": "sha256-l/iNYDZ4bGOAFQY2q8y5OAfBBtrDAaPuRQqWaFHVRXM=",
+        "lastModified": 1777954456,
+        "narHash": "sha256-hGdgeU2Nk87RAuZyYjyDjFL6LK7dAZN5RE9+hrDTkDU=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "4bd9165a9165d7b5e33ae57f3eecbcb28fb231c9",
+        "rev": "549bd84d6279f9852cae6225e372cc67fb91a4c1",
         "type": "github"
       },
       "original": {
@@ -55,15 +55,16 @@
     "plugins-r": {
       "flake": false,
       "locked": {
-        "lastModified": 1776340770,
-        "narHash": "sha256-o/8UZIc/Bq9dWTjA+MpSR5uMUpE7KHTErk+TwWID8Ww=",
+        "lastModified": 1776905071,
+        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
         "owner": "R-nvim",
         "repo": "R.nvim",
-        "rev": "b9cfffeb9b4e484aa9e13f01c0eb80230aada455",
+        "rev": "582f2af11290ac067e49018db38e12a511325556",
         "type": "github"
       },
       "original": {
         "owner": "R-nvim",
+        "ref": "v0.99.4",
         "repo": "R.nvim",
         "type": "github"
       }
@@ -101,11 +102,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1776375800,
-        "narHash": "sha256-/SSAR77Brr9fbapsh1cb2K47JXCbvwS1GjM4yyDxle8=",
+        "lastModified": 1777991014,
+        "narHash": "sha256-0DS24OW9d9iz+w0LCz6KpS2IpE2z2gHxeBdMZg9xpDY=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "f11469ca69068bac13d9e163b2bd268cc06dff57",
+        "rev": "dc5184095ad488e937ec308b52c9c0b218959d8b",
         "type": "github"
       },
       "original": {
diff --git a/flake.nix b/flake.nix
index f7db07c..8482605 100644
--- a/flake.nix
+++ b/flake.nix
@@ -20,7 +20,7 @@
     };
 
     "plugins-r" = {
-      url = "github:R-nvim/R.nvim";
+      url = "github:R-nvim/R.nvim/v0.99.4";
       flake = false;
     };
 

From 07d2156dfb4620e8e18b4d1244a17b7fde4f91da Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Tue, 12 May 2026 15:58:31 +1000
Subject: [PATCH 04/28] fixed R.nvim

---
 .commandcode/taste/taste.md      |  8 ++++++++
 flake.nix                        | 13 ++++++++++---
 modules/module/settings/cats.nix |  2 +-
 modules/module/settings/env.nix  |  7 ++++++-
 modules/module/specs/plugins.nix |  8 +++++++-
 overlays/r.nix                   | 28 +++++++++++++++++++++++++++-
 plugin/21_datascience.lua        |  6 ++++++
 7 files changed, 65 insertions(+), 7 deletions(-)
 create mode 100644 .commandcode/taste/taste.md

diff --git a/.commandcode/taste/taste.md b/.commandcode/taste/taste.md
new file mode 100644
index 0000000..4b588b2
--- /dev/null
+++ b/.commandcode/taste/taste.md
@@ -0,0 +1,8 @@
+# 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
+
+# Taste (Continuously Learned by [CommandCode][cmd])
+
+[cmd]: https://commandcode.ai/
+
diff --git a/flake.nix b/flake.nix
index 8482605..be28255 100644
--- a/flake.nix
+++ b/flake.nix
@@ -46,7 +46,7 @@
         nix = true;
         optional = false;
         python = false;
-        r = false;
+        r = true;
       };
       settings = {
         lang_packages = {
@@ -199,7 +199,8 @@
           zk
         ];
 
-        shellPackages = [nvimPkg]
+        shellPackages =
+          [nvimPkg]
           ++ pkgs.lib.optionals cfg.cats.python pythonPackages
           ++ pkgs.lib.optionals cfg.cats.r rPackages
           ++ pkgs.lib.optionals cfg.cats.julia juliaPackages
@@ -210,7 +211,13 @@
           packages = shellPackages;
           nativeBuildInputs = with pkgs; [] ++ (pkgs.lib.optionals cfg.cats.optional [devenv]);
           inputsFrom = [];
-          shellHook = "";
+          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 "$R_LIBS_USER"
+          '';
         };
       }
     );
diff --git a/modules/module/settings/cats.nix b/modules/module/settings/cats.nix
index 22b3638..3da043e 100644
--- a/modules/module/settings/cats.nix
+++ b/modules/module/settings/cats.nix
@@ -43,7 +43,7 @@
     nix = lib.mkDefault true;
     optional = lib.mkDefault false;
     python = lib.mkDefault false;
-    r = lib.mkDefault false;
+    r = lib.mkDefault true;
     test = lib.mkDefault false;
     treesitterParsers = lib.mkDefault true;
     utils = lib.mkDefault true;
diff --git a/modules/module/settings/env.nix b/modules/module/settings/env.nix
index 2ae4b9c..0749ede 100644
--- a/modules/module/settings/env.nix
+++ b/modules/module/settings/env.nix
@@ -11,12 +11,17 @@
       UV_PYTHON_DOWNLOADS = "never";
       UV_PYTHON = pkgs.python.interpreter;
     })
+    (lib.mkIf (config.cats.r or false) {
+      RNVIM_COMPLDIR = "$PWD/.r-compl";
+      R_LIBS_USER = "${pkgs.nvimcom}:$PWD/.Rlibs";
+      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 =  "./.Rlibs";
+      R_LIBS_USER =  "${pkgs.nvimcom}:$PWD/.Rlibs";
     })
   ];
 }
diff --git a/modules/module/specs/plugins.nix b/modules/module/specs/plugins.nix
index ded8195..eb9d499 100644
--- a/modules/module/specs/plugins.nix
+++ b/modules/module/specs/plugins.nix
@@ -11,7 +11,13 @@
 
   config.specs.r = {
     data = with pkgs.vimPlugins; [
-      config.nvim-lib.neovimPlugins.r
+      (config.nvim-lib.neovimPlugins.r.overrideAttrs (old: {
+        postInstall = (old.postInstall or "") + ''
+          mkdir -p $out/rnvimserver
+          cp ${pkgs.nvimcom}/bin/rnvimserver $out/rnvimserver/rnvimserver
+          chmod +x $out/rnvimserver/rnvimserver
+        '';
+      }))
       quarto-nvim
       {
         data = otter-nvim;
diff --git a/overlays/r.nix b/overlays/r.nix
index 2fb71c8..22c42fa 100644
--- a/overlays/r.nix
+++ b/overlays/r.nix
@@ -33,12 +33,38 @@
     overlays = [inputs.fran.overlays.default];
   }; # rixpkgs.legacyPackages.${prev.stdenv.hostPlatform.system};
 
+  # Pre-build nvimcom from R.nvim plugin source so R.nvim never tries to
+  # compile it at runtime into the read-only nix store.
+  nvimcom = final.stdenv.mkDerivation {
+    pname = "nvimcom";
+    version = "0.9.92";
+    src = inputs.plugins-r;
+    nativeBuildInputs = [
+      (rpkgs.rWrapper.override { packages = []; })
+    ];
+    buildPhase = ''
+      mkdir -p $out/bin
+      R CMD INSTALL -l $out nvimcom
+      cd rnvimserver
+      $CC -pthread -O2 -Wall \
+        complete.c resolve.c hover.c definition.c signature.c \
+        rhelp.c chunk.c roxygen.c data_structures.c logging.c \
+        rnvimserver.c obbr.c tcp.c utilities.c ../nvimcom/src/common.c \
+        -o $out/bin/rnvimserver
+      cd ..
+      mkdir -p $out/nvimcom/bin
+      cp $out/bin/rnvimserver $out/nvimcom/bin/rnvimserver
+      chmod +x $out/bin/rnvimserver $out/nvimcom/bin/rnvimserver
+    '';
+    installPhase = "true";
+  };
+
   # Standard R packages used by default in rWrapper and quarto
   reqPkgs = with rpkgs.rPackages; [
     #    languageserver
   ];
 in {
-  inherit rpkgs;
+  inherit rpkgs nvimcom;
   baseRPackages = reqPkgs;
 
   # R wrapper with standard packages
diff --git a/plugin/21_datascience.lua b/plugin/21_datascience.lua
index 118ee20..62d8f49 100644
--- a/plugin/21_datascience.lua
+++ b/plugin/21_datascience.lua
@@ -44,6 +44,12 @@ end)
 -- r
 now(function()
   if nix.get_cat("r", false) then
+    local cwd = vim.fn.getcwd(-1)
+    vim.env.RNVIM_COMPLDIR = cwd .. "/.r-compl"
+    vim.env.R_LIBS_USER = (vim.env.R_LIBS_USER or ""):gsub("%$PWD", cwd)
+    vim.env.TMPDIR = cwd .. "/.r-tmp"
+    vim.fn.mkdir(vim.env.RNVIM_COMPLDIR, "p")
+    vim.fn.mkdir(vim.env.TMPDIR, "p")
     vim.g.rout_follow_colorscheme = true
     require("r").setup({
       -- Create a table with the options to be passed to setup()

From 1055522af932f5c781ff475cb390143534d49141 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Wed, 13 May 2026 12:30:17 +1000
Subject: [PATCH 05/28] moved r-nvim to flake build

---
 .Rprofile                               |  5 ++++
 .r-tmp/R.nvim-daniel/globenv_1202824815 |  0
 .r-tmp/R.nvim-daniel/liblist_1202824815 |  0
 flake.lock                              | 38 ++++++++++++++++++++-----
 flake.nix                               |  9 +++++-
 modules/module/settings/env.nix         |  4 +--
 modules/module/specs/plugins.nix        |  2 +-
 overlays/default.nix                    |  4 +++
 overlays/r.nix                          | 29 ++-----------------
 9 files changed, 54 insertions(+), 37 deletions(-)
 create mode 100644 .Rprofile
 create mode 100644 .r-tmp/R.nvim-daniel/globenv_1202824815
 create mode 100644 .r-tmp/R.nvim-daniel/liblist_1202824815

diff --git a/.Rprofile b/.Rprofile
new file mode 100644
index 0000000..7617f61
--- /dev/null
+++ b/.Rprofile
@@ -0,0 +1,5 @@
+if (Sys.getenv("RNVIM_TMPDIR") == "") {
+  options(defaultPackages = c("utils", "grDevices", "graphics", "stats", "methods"))
+} else {
+  options(defaultPackages = c("utils", "grDevices", "graphics", "stats", "methods", "nvimcom"))
+}
diff --git a/.r-tmp/R.nvim-daniel/globenv_1202824815 b/.r-tmp/R.nvim-daniel/globenv_1202824815
new file mode 100644
index 0000000..e69de29
diff --git a/.r-tmp/R.nvim-daniel/liblist_1202824815 b/.r-tmp/R.nvim-daniel/liblist_1202824815
new file mode 100644
index 0000000..e69de29
diff --git a/flake.lock b/flake.lock
index 32a6765..bf489c1 100644
--- a/flake.lock
+++ b/flake.lock
@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1777954456,
-        "narHash": "sha256-hGdgeU2Nk87RAuZyYjyDjFL6LK7dAZN5RE9+hrDTkDU=",
+        "lastModified": 1778443072,
+        "narHash": "sha256-zi7/fsqM/kFdNuED//4WOCUtezGtKKqRNORjMvfwjnA=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "549bd84d6279f9852cae6225e372cc67fb91a4c1",
+        "rev": "da5ad661ba4e5ef59ba743f0d112cbc30e474f32",
         "type": "github"
       },
       "original": {
@@ -69,6 +69,29 @@
         "type": "github"
       }
     },
+    "r-nvim-nix": {
+      "inputs": {
+        "nixpkgs": [
+          "rixpkgs"
+        ],
+        "rnvimsrc": [
+          "plugins-r"
+        ]
+      },
+      "locked": {
+        "lastModified": 1778638679,
+        "narHash": "sha256-+mdjgYfyNtI/5E6X8uUx3u9qpGC9POS4LagOHSM3Iy0=",
+        "owner": "dwinkler1",
+        "repo": "r_nvim_nix",
+        "rev": "eb784558e18b8f1dead5bd211b96fd287ac1bed7",
+        "type": "github"
+      },
+      "original": {
+        "owner": "dwinkler1",
+        "repo": "r_nvim_nix",
+        "type": "github"
+      }
+    },
     "rixpkgs": {
       "locked": {
         "lastModified": 1771303851,
@@ -80,8 +103,8 @@
       },
       "original": {
         "owner": "dwinkler1",
-        "ref": "nixpkgs",
         "repo": "rixpkgs",
+        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
         "type": "github"
       }
     },
@@ -91,6 +114,7 @@
         "nixpkgs": "nixpkgs",
         "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
         "plugins-r": "plugins-r",
+        "r-nvim-nix": "r-nvim-nix",
         "rixpkgs": "rixpkgs",
         "wrappers": "wrappers"
       }
@@ -102,11 +126,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1777991014,
-        "narHash": "sha256-0DS24OW9d9iz+w0LCz6KpS2IpE2z2gHxeBdMZg9xpDY=",
+        "lastModified": 1778560014,
+        "narHash": "sha256-Hu9RMo7vJt/4dx/vAvyG+cE9RBwpaH1ouyunvruYaDI=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "dc5184095ad488e937ec308b52c9c0b218959d8b",
+        "rev": "e30aa99c9c7038e16efae3cad7916a47307a9e36",
         "type": "github"
       },
       "original": {
diff --git a/flake.nix b/flake.nix
index be28255..1ffa69a 100644
--- a/flake.nix
+++ b/flake.nix
@@ -10,7 +10,11 @@
       url = "github:BirdeeHub/nix-wrapper-modules";
       inputs.nixpkgs.follows = "nixpkgs";
     };
-    rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs";
+    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";
 
     fran = {
       url = "github:dwinkler1/fran";
@@ -61,6 +65,7 @@
             janitor
             languageserver
             styler
+            pkgs.nvimcom
           ];
           julia = ["DataFramesMeta" "QuackIO"];
         };
@@ -187,6 +192,8 @@
             air-formatter
             yaml-language-server
             updateR
+            nvimcom
+            rnvimserver
           ];
 
         juliaPackages = let
diff --git a/modules/module/settings/env.nix b/modules/module/settings/env.nix
index 0749ede..14e0a32 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}:$PWD/.Rlibs";
+      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
       TMPDIR = "$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 =  "${pkgs.nvimcom}:$PWD/.Rlibs";
+      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
     })
   ];
 }
diff --git a/modules/module/specs/plugins.nix b/modules/module/specs/plugins.nix
index eb9d499..a47ba65 100644
--- a/modules/module/specs/plugins.nix
+++ b/modules/module/specs/plugins.nix
@@ -14,7 +14,7 @@
       (config.nvim-lib.neovimPlugins.r.overrideAttrs (old: {
         postInstall = (old.postInstall or "") + ''
           mkdir -p $out/rnvimserver
-          cp ${pkgs.nvimcom}/bin/rnvimserver $out/rnvimserver/rnvimserver
+          cp ${pkgs.rnvimserver}/bin/rnvimserver $out/rnvimserver/rnvimserver
           chmod +x $out/rnvimserver/rnvimserver
         '';
       }))
diff --git a/overlays/default.nix b/overlays/default.nix
index 821ff88..ebb6518 100644
--- a/overlays/default.nix
+++ b/overlays/default.nix
@@ -3,12 +3,14 @@ let
   lib = nixpkgs.lib;
 
   rOverlay = import ./r.nix {inherit inputs;};
+  rNvimNixOverlay = inputs.r-nvim-nix.overlays.default;
   franOverlay = inputs.fran.overlays.default;
   pythonOverlay = import ./python.nix inputs;
   pluginsOverlay = import ./plugins.nix inputs;
 
   dependencyOverlays = [
     rOverlay
+    rNvimNixOverlay
     pythonOverlay
     pluginsOverlay
   ];
@@ -17,6 +19,7 @@ in
 {
   inherit
     rOverlay
+    rNvimNixOverlay
     franOverlay
     pythonOverlay
     pluginsOverlay
@@ -30,6 +33,7 @@ in
   overlays = {
     inherit
       rOverlay
+      rNvimNixOverlay
       franOverlay
       pythonOverlay
       pluginsOverlay
diff --git a/overlays/r.nix b/overlays/r.nix
index 22c42fa..a9961fb 100644
--- a/overlays/r.nix
+++ b/overlays/r.nix
@@ -33,38 +33,15 @@
     overlays = [inputs.fran.overlays.default];
   }; # rixpkgs.legacyPackages.${prev.stdenv.hostPlatform.system};
 
-  # Pre-build nvimcom from R.nvim plugin source so R.nvim never tries to
-  # compile it at runtime into the read-only nix store.
-  nvimcom = final.stdenv.mkDerivation {
-    pname = "nvimcom";
-    version = "0.9.92";
-    src = inputs.plugins-r;
-    nativeBuildInputs = [
-      (rpkgs.rWrapper.override { packages = []; })
-    ];
-    buildPhase = ''
-      mkdir -p $out/bin
-      R CMD INSTALL -l $out nvimcom
-      cd rnvimserver
-      $CC -pthread -O2 -Wall \
-        complete.c resolve.c hover.c definition.c signature.c \
-        rhelp.c chunk.c roxygen.c data_structures.c logging.c \
-        rnvimserver.c obbr.c tcp.c utilities.c ../nvimcom/src/common.c \
-        -o $out/bin/rnvimserver
-      cd ..
-      mkdir -p $out/nvimcom/bin
-      cp $out/bin/rnvimserver $out/nvimcom/bin/rnvimserver
-      chmod +x $out/bin/rnvimserver $out/nvimcom/bin/rnvimserver
-    '';
-    installPhase = "true";
-  };
+  # nvimcom and rnvimserver are provided by the r-nvim-nix flake overlay
+  # (inputs.r-nvim-nix.overlays.default)
 
   # Standard R packages used by default in rWrapper and quarto
   reqPkgs = with rpkgs.rPackages; [
     #    languageserver
   ];
 in {
-  inherit rpkgs nvimcom;
+  inherit rpkgs;
   baseRPackages = reqPkgs;
 
   # R wrapper with standard packages

From 55866137ba5379c266defbb50f3fd9b40fe1a8b2 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Wed, 13 May 2026 12:30:36 +1000
Subject: [PATCH 06/28] cleanup

---
 .r-tmp/R.nvim-daniel/globenv_1202824815 | 0
 .r-tmp/R.nvim-daniel/liblist_1202824815 | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 .r-tmp/R.nvim-daniel/globenv_1202824815
 delete mode 100644 .r-tmp/R.nvim-daniel/liblist_1202824815

diff --git a/.r-tmp/R.nvim-daniel/globenv_1202824815 b/.r-tmp/R.nvim-daniel/globenv_1202824815
deleted file mode 100644
index e69de29..0000000
diff --git a/.r-tmp/R.nvim-daniel/liblist_1202824815 b/.r-tmp/R.nvim-daniel/liblist_1202824815
deleted file mode 100644
index e69de29..0000000

From 22809d94cd5f03cde3150d93b6e3b385cca738f6 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Wed, 13 May 2026 13:28:55 +1000
Subject: [PATCH 07/28] update

---
 flake.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/flake.lock b/flake.lock
index bf489c1..7f552ab 100644
--- a/flake.lock
+++ b/flake.lock
@@ -79,11 +79,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1778638679,
-        "narHash": "sha256-+mdjgYfyNtI/5E6X8uUx3u9qpGC9POS4LagOHSM3Iy0=",
+        "lastModified": 1778641093,
+        "narHash": "sha256-Cq0spPQCYJkyHFTBTXqjmbq663kIVZA63/TQkTzE4ps=",
         "owner": "dwinkler1",
         "repo": "r_nvim_nix",
-        "rev": "eb784558e18b8f1dead5bd211b96fd287ac1bed7",
+        "rev": "435103d25d56dbe43197f7969cf535fda17ff597",
         "type": "github"
       },
       "original": {

From 8811591fe0eabed342283e897bc25536a67fdca4 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Thu, 14 May 2026 00:52:03 +1000
Subject: [PATCH 08/28] Move to bundled R.nvim + rnvimserver without override

---
 flake.lock                       | 12 ++++++------
 modules/module/specs/plugins.nix |  8 +-------
 2 files changed, 7 insertions(+), 13 deletions(-)

diff --git a/flake.lock b/flake.lock
index 7f552ab..73686b6 100644
--- a/flake.lock
+++ b/flake.lock
@@ -79,11 +79,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1778641093,
-        "narHash": "sha256-Cq0spPQCYJkyHFTBTXqjmbq663kIVZA63/TQkTzE4ps=",
+        "lastModified": 1778683425,
+        "narHash": "sha256-bY44RR+7q+8R8PDNWbavFEcpSKiBvWyoWHI7iSLvsQc=",
         "owner": "dwinkler1",
         "repo": "r_nvim_nix",
-        "rev": "435103d25d56dbe43197f7969cf535fda17ff597",
+        "rev": "e54fb57802fa9eca81024762f397ec7caa446842",
         "type": "github"
       },
       "original": {
@@ -126,11 +126,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1778560014,
-        "narHash": "sha256-Hu9RMo7vJt/4dx/vAvyG+cE9RBwpaH1ouyunvruYaDI=",
+        "lastModified": 1778662548,
+        "narHash": "sha256-e6XKnrzKr48r1UdCr+5bekibSqe2L1/Sgi46IODHtGQ=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "e30aa99c9c7038e16efae3cad7916a47307a9e36",
+        "rev": "46e7c1e3f0e149b28f539eb8601152db8a67ad0c",
         "type": "github"
       },
       "original": {
diff --git a/modules/module/specs/plugins.nix b/modules/module/specs/plugins.nix
index a47ba65..ca8d970 100644
--- a/modules/module/specs/plugins.nix
+++ b/modules/module/specs/plugins.nix
@@ -11,13 +11,7 @@
 
   config.specs.r = {
     data = with pkgs.vimPlugins; [
-      (config.nvim-lib.neovimPlugins.r.overrideAttrs (old: {
-        postInstall = (old.postInstall or "") + ''
-          mkdir -p $out/rnvimserver
-          cp ${pkgs.rnvimserver}/bin/rnvimserver $out/rnvimserver/rnvimserver
-          chmod +x $out/rnvimserver/rnvimserver
-        '';
-      }))
+      pkgs.r-nvim
       quarto-nvim
       {
         data = otter-nvim;

From 4d28d0d4907c2d3d20bdf0c5b2482ccc860114dc Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Tue, 19 May 2026 13:15:29 +1000
Subject: [PATCH 09/28] fix for codecompanion

---
 flake.lock                       | 18 +++++++++---------
 flake.nix                        |  2 +-
 modules/module/specs/plugins.nix | 11 ++++++-----
 3 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/flake.lock b/flake.lock
index 73686b6..9fbb80f 100644
--- a/flake.lock
+++ b/flake.lock
@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1778443072,
-        "narHash": "sha256-zi7/fsqM/kFdNuED//4WOCUtezGtKKqRNORjMvfwjnA=",
+        "lastModified": 1778869304,
+        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "da5ad661ba4e5ef59ba743f0d112cbc30e474f32",
+        "rev": "d233902339c02a9c334e7e593de68855ad26c4cb",
         "type": "github"
       },
       "original": {
@@ -79,11 +79,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1778683425,
-        "narHash": "sha256-bY44RR+7q+8R8PDNWbavFEcpSKiBvWyoWHI7iSLvsQc=",
+        "lastModified": 1778684156,
+        "narHash": "sha256-Z4y1tQfkIsPK4NRxGn668HMDfWxnxNxSJ0CAOOXiIfY=",
         "owner": "dwinkler1",
         "repo": "r_nvim_nix",
-        "rev": "e54fb57802fa9eca81024762f397ec7caa446842",
+        "rev": "2f49dfee27886068e2f49cbd54558ce4cc424c82",
         "type": "github"
       },
       "original": {
@@ -126,11 +126,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1778662548,
-        "narHash": "sha256-e6XKnrzKr48r1UdCr+5bekibSqe2L1/Sgi46IODHtGQ=",
+        "lastModified": 1779145538,
+        "narHash": "sha256-j2RQqBLYhPuddU6C8n5hGKboXq1tDLCZ7bWe5/LgTHM=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "46e7c1e3f0e149b28f539eb8601152db8a67ad0c",
+        "rev": "597b35c93dd0ab0ae38758e3193582b2fd259aa1",
         "type": "github"
       },
       "original": {
diff --git a/flake.nix b/flake.nix
index 1ffa69a..fa1140a 100644
--- a/flake.nix
+++ b/flake.nix
@@ -105,7 +105,7 @@
     forAllSystems = nixpkgs.lib.genAttrs systems;
 
     extra_pkg_config = {
-      # allowUnfree = true;
+       allowUnfree = true;
     };
 
     overlayDefs = import ./overlays inputs;
diff --git a/modules/module/specs/plugins.nix b/modules/module/specs/plugins.nix
index ca8d970..431005d 100644
--- a/modules/module/specs/plugins.nix
+++ b/modules/module/specs/plugins.nix
@@ -3,10 +3,9 @@
   pkgs,
   lib,
   ...
-}:
-{
+}: {
   config.specs.gitPlugins = {
-    data = [ ];
+    data = [];
   };
 
   config.specs.r = {
@@ -112,7 +111,9 @@
       nvim-treesitter-context
       nvim-treesitter-textobjects
       {
-        data = pkgs.codecompanion-nvim;
+        data = pkgs.codecompanion-nvim.overrideAttrs (old: {
+          doCheck = false;
+        });
         pname = "codecompanion";
       }
     ];
@@ -176,6 +177,6 @@
 
   config.specs.gitPlugins-lazy = {
     lazy = true;
-    data = [ ];
+    data = [];
   };
 }

From bfd4ba417d3f385436974b5388981994116a13d0 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Tue, 19 May 2026 13:18:29 +1000
Subject: [PATCH 10/28] remove languageserver package from config

---
 plugin/25_lsp.lua | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/plugin/25_lsp.lua b/plugin/25_lsp.lua
index 9591da3..8c67295 100644
--- a/plugin/25_lsp.lua
+++ b/plugin/25_lsp.lua
@@ -15,17 +15,17 @@ now_if_args(function()
     marksman = {
       filetypes = { "markdown", "markdown_inline", "codecompanion" },
     },
-    r_language_server = {
-      filetypes = { 'r', 'rmd', 'rmarkdown' },
-      settings = {
-        ['r_language_server'] = {
-          lsp = {
-            rich_documentation = true,
-            enable = true,
-          },
-        },
-      }
-    },
+    -- r_language_server = {
+    --   filetypes = { 'r', 'rmd', 'rmarkdown' },
+    --   settings = {
+    --     ['r_language_server'] = {
+    --       lsp = {
+    --         rich_documentation = true,
+    --         enable = true,
+    --       },
+    --     },
+    --   }
+    -- },
     julials = {
       settings = {
         julia = {

From ad9473a9166fc7e220449c9fd7625f8c52e05423 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Tue, 19 May 2026 13:28:40 +1000
Subject: [PATCH 11/28] different ls

---
 plugin/25_lsp.lua | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/plugin/25_lsp.lua b/plugin/25_lsp.lua
index 8c67295..f3c4c50 100644
--- a/plugin/25_lsp.lua
+++ b/plugin/25_lsp.lua
@@ -15,17 +15,17 @@ now_if_args(function()
     marksman = {
       filetypes = { "markdown", "markdown_inline", "codecompanion" },
     },
-    -- r_language_server = {
-    --   filetypes = { 'r', 'rmd', 'rmarkdown' },
-    --   settings = {
-    --     ['r_language_server'] = {
-    --       lsp = {
-    --         rich_documentation = true,
-    --         enable = true,
-    --       },
-    --     },
-    --   }
-    -- },
+    r_ls = {
+      filetypes = { 'r', 'rmd', 'rmarkdown' },
+      settings = {
+        ['r_ls'] = {
+          lsp = {
+            rich_documentation = true,
+            enable = true,
+          },
+        },
+      }
+    },
     julials = {
       settings = {
         julia = {

From 74600519a5f4a73a96b44156b2f4c5b273d2268b Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Thu, 21 May 2026 18:45:36 +1000
Subject: [PATCH 12/28] Simplified codebase

---
 .commandcode/taste/taste.md               |   1 +
 flake.lock                                |   6 +-
 flake.nix                                 | 105 ++++++++--------------
 modules/module/settings/cats.nix          |   6 +-
 modules/module/settings/core.nix          |   6 +-
 modules/module/settings/env.nix           |   6 +-
 modules/module/settings/hosts.nix         |   2 +-
 modules/module/settings/lang-packages.nix |   2 +-
 modules/module/settings/runtime-path.nix  |   4 +-
 modules/module/specs/cats-enable.nix      |  51 -----------
 modules/module/specs/deps.nix             |  66 +++-----------
 modules/module/specs/plugins.nix          |  20 ++---
 modules/neovim.nix                        |  16 ----
 overlays/default.nix                      |  24 ++---
 overlays/r.nix                            |  48 +---------
 15 files changed, 83 insertions(+), 280 deletions(-)
 delete mode 100644 modules/module/specs/cats-enable.nix

diff --git a/.commandcode/taste/taste.md b/.commandcode/taste/taste.md
index 4b588b2..54e4488 100644
--- a/.commandcode/taste/taste.md
+++ b/.commandcode/taste/taste.md
@@ -1,6 +1,7 @@
 # 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])
 
diff --git a/flake.lock b/flake.lock
index 9fbb80f..698ccf9 100644
--- a/flake.lock
+++ b/flake.lock
@@ -126,11 +126,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1779145538,
-        "narHash": "sha256-j2RQqBLYhPuddU6C8n5hGKboXq1tDLCZ7bWe5/LgTHM=",
+        "lastModified": 1779297405,
+        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "597b35c93dd0ab0ae38758e3193582b2fd259aa1",
+        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
         "type": "github"
       },
       "original": {
diff --git a/flake.nix b/flake.nix
index fa1140a..f84715f 100644
--- a/flake.nix
+++ b/flake.nix
@@ -1,11 +1,10 @@
-# Copyright (c) 2026 BirdeeHub
+# Copyright (c) 2026 Daniel
 # Licensed under the MIT license
 {
   description = "Daniel's NixCats";
 
   inputs = {
     nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable";
-    #nixpkgs.url = "github:nixos/nixpkgs/nixos-25.11";
     wrappers = {
       url = "github:BirdeeHub/nix-wrapper-modules";
       inputs.nixpkgs.follows = "nixpkgs";
@@ -40,13 +39,15 @@
     wrappers,
     ...
   } @ inputs: let
-    mkWrapperConfig = pkgs: {
-      cats = {
+    mkWrapperConfig = pkgs: let
+      def = pkgs.lib.mkDefault;
+    in {
+      cats = pkgs.lib.mapAttrs (_: v: def v) {
         clickhouse = false;
         gitPlugins = true;
         julia = false;
         lua = true;
-        markdown = false;
+        markdown = true;
         nix = true;
         optional = false;
         python = false;
@@ -54,46 +55,30 @@
       };
       settings = {
         lang_packages = {
-          python = with pkgs.python3Packages; [
+          python = def (with pkgs.python3Packages; [
             duckdb
             polars
-          ];
-          r = with pkgs.rpkgs.rPackages; [
+          ]);
+          r = def ((with pkgs.rpkgs.rPackages; [
             arrow
             broom
             data_table
             janitor
             languageserver
             styler
-            pkgs.nvimcom
-          ];
-          julia = ["DataFramesMeta" "QuackIO"];
+          ]) ++ [ pkgs.nvimcom ]);
+          julia = def ["DataFramesMeta" "QuackIO"];
         };
-        colorscheme = "cyberdream";
-        background = "dark";
-        wrapRc = true;
       };
-      binName = "vv";
+      binName = def "vv";
     };
 
     wrapperSettings = pkgs: let
       cfg = mkWrapperConfig pkgs;
-      def = pkgs.lib.mkDefault;
     in
       wrapper.config.wrap {
         inherit pkgs;
-        cats = pkgs.lib.mapAttrs (_: v: def v) cfg.cats;
-        settings = {
-          lang_packages = {
-            python = def cfg.settings.lang_packages.python;
-            r = def cfg.settings.lang_packages.r;
-            julia = def cfg.settings.lang_packages.julia;
-          };
-          colorscheme = def cfg.settings.colorscheme;
-          background = def cfg.settings.background;
-          wrapRc = def cfg.settings.wrapRc;
-        };
-        binName = def cfg.binName;
+        inherit (cfg) cats settings binName;
       };
 
     systems = [
@@ -104,54 +89,39 @@
 
     forAllSystems = nixpkgs.lib.genAttrs systems;
 
-    extra_pkg_config = {
-       allowUnfree = true;
-    };
-
     overlayDefs = import ./overlays inputs;
 
-    dependencyOverlays = overlayDefs.dependencyOverlays;
-
-    dependencyOverlay = overlayDefs.dependencyOverlay;
-
     mkPkgs = system:
       import nixpkgs {
         inherit system;
-        config = extra_pkg_config;
-        overlays = [dependencyOverlay];
+        config = { allowUnfree = true; };
+        overlays = [ overlayDefs.dependencyOverlay ];
       };
 
-    module = nixpkgs.lib.modules.importApply ./modules/neovim.nix inputs;
+    module = (import ./modules/neovim.nix) inputs;
     wrapper = wrappers.lib.evalModule module;
   in {
     overlays = {
+      # overlay `vv` wraps the module with default settings only.
+      # For the fully-configured binary (including mkWrapperConfig overrides),
+      # use `packages.<system>.default` instead.
       default = nixpkgs.lib.composeManyExtensions [
-        dependencyOverlay
+        overlayDefs.dependencyOverlay
         (final: prev: {
           vv = wrapper.config.wrap {pkgs = final;};
         })
       ];
-      dependencies = dependencyOverlay;
-      vv = self.overlays.default;
+      dependencies = overlayDefs.dependencyOverlay;
     };
 
-    wrapperModules = {
-      default = module;
-      neovim = self.wrapperModules.default;
-    };
-
-    wrappers = {
-      default = wrapper.config;
-      neovim = self.wrappers.default;
-    };
+    wrapperModules.default = module;
+    wrapperConfigs.default = wrapper.config;
 
     packages = forAllSystems (
       system: let
         pkgs = mkPkgs system;
-        nvimPkg = wrapperSettings pkgs;
       in {
-        default = nvimPkg;
-        vv = nvimPkg;
+        default = wrapperSettings pkgs;
       }
     );
 
@@ -208,16 +178,15 @@
 
         shellPackages =
           [nvimPkg]
-          ++ pkgs.lib.optionals cfg.cats.python pythonPackages
-          ++ pkgs.lib.optionals cfg.cats.r rPackages
-          ++ pkgs.lib.optionals cfg.cats.julia juliaPackages
-          ++ pkgs.lib.optionals cfg.cats.markdown markdownPackages;
+          ++ 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;
       in {
         default = pkgs.mkShell {
           name = "vShell";
           packages = shellPackages;
-          nativeBuildInputs = with pkgs; [] ++ (pkgs.lib.optionals cfg.cats.optional [devenv]);
-          inputsFrom = [];
+          nativeBuildInputs = pkgs.lib.optionals wrapper.config.cats.optional [ pkgs.devenv ];
           shellHook = ''
             echo 'I am a NixShell'
             export R_HOME=$(R RHOME)
@@ -234,18 +203,11 @@
         pkgs = mkPkgs system;
         nvimPkg = wrapperSettings pkgs;
       in {
-        default = nvimPkg;
-        module-eval = let
-          _ = wrapper.config;
-        in
-          pkgs.runCommand "check-module-eval" {} ''
-            echo "Module evaluation successful" > $out
-          '';
-        package-build = pkgs.runCommand "check-vv" {} ''
+        default = pkgs.runCommand "check-vv" {} ''
           BINARY_PATH="${nvimPkg}/bin/vv"
 
           if [ ! -x "$BINARY_PATH" ]; then
-            echo "Error: Binary n not found or not executable"
+            echo "Error: Binary not found or not executable"
             exit 1
           fi
 
@@ -258,6 +220,11 @@
             cat version_output.txt >> $out
           fi
         '';
+        module-eval =
+          let _ = wrapper.config;
+          in pkgs.runCommand "check-module-eval" {} ''
+            echo "Module evaluation successful" > $out
+          '';
       }
     );
 
diff --git a/modules/module/settings/cats.nix b/modules/module/settings/cats.nix
index 3da043e..13758d4 100644
--- a/modules/module/settings/cats.nix
+++ b/modules/module/settings/cats.nix
@@ -14,7 +14,6 @@
 
       Available categories:
       - clickhouse: Clickhouse client and tools
-      - customPlugins: local plugin specs
       - external: external tools and integrations
       - general: core Neovim plugins/features
       - gitPlugins: git-related plugins
@@ -25,7 +24,6 @@
       - optional: optional tools and utilities
       - python: Python tooling and plugins
       - r: R tooling and plugins
-      - test: test-only tooling (disabled by default)
       - treesitterParsers: Treesitter parsers
       - utils: general utilities
     '';
@@ -33,18 +31,16 @@
 
   config.cats = {
     clickhouse = lib.mkDefault false;
-    customPlugins = lib.mkDefault true;
     external = lib.mkDefault true;
     general = lib.mkDefault true;
     gitPlugins = lib.mkDefault true;
     julia = lib.mkDefault false;
     lua = lib.mkDefault true;
-    markdown = lib.mkDefault false;
+    markdown = lib.mkDefault true;
     nix = lib.mkDefault true;
     optional = lib.mkDefault false;
     python = lib.mkDefault false;
     r = lib.mkDefault true;
-    test = lib.mkDefault false;
     treesitterParsers = lib.mkDefault true;
     utils = lib.mkDefault true;
   };
diff --git a/modules/module/settings/core.nix b/modules/module/settings/core.nix
index 42e9e11..ec9bb5c 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 false) [ lp.tiktoken_core ];
+    lib.optionals (config.cats.general or true) [ lp.tiktoken_core ];
 
   # Binary name for the wrapper
   config.binName = lib.mkDefault "vv";
@@ -25,10 +25,10 @@
   config.settings.block_normal_config = true;
 
   # Don't symlink the config (we wrap it instead)
-  config.settings.dont_link = false;
+  config.settings.dont_link = lib.mkDefault false;
 
   # Create additional aliases for the binary
-  config.settings.aliases = [ "vvim" ];
+  config.settings.aliases = lib.mkDefault [ "vvim" ];
 
   # Enable wrapper handling of spec runtimeDeps (template pattern).
   config.settings.autowrapRuntimeDeps = true;
diff --git a/modules/module/settings/env.nix b/modules/module/settings/env.nix
index 14e0a32..2fcab8a 100644
--- a/modules/module/settings/env.nix
+++ b/modules/module/settings/env.nix
@@ -7,11 +7,11 @@
   # Environment variables set for the wrapper.
   # These are available when running neovim.
   config.env = lib.mkMerge [
-    (lib.mkIf (config.cats.python or false) {
+    (lib.mkIf (config.cats.python or true) {
       UV_PYTHON_DOWNLOADS = "never";
       UV_PYTHON = pkgs.python.interpreter;
     })
-    (lib.mkIf (config.cats.r or false) {
+    (lib.mkIf (config.cats.r or true) {
       RNVIM_COMPLDIR = "$PWD/.r-compl";
       R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
       TMPDIR = "$PWD/.r-tmp";
@@ -20,7 +20,7 @@
 
   # Environment variables with defaults (can be overridden by user)
   config.envDefault = lib.mkMerge [
-    (lib.mkIf (config.cats.r or false) {
+    (lib.mkIf (config.cats.r or true) {
       R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
     })
   ];
diff --git a/modules/module/settings/hosts.nix b/modules/module/settings/hosts.nix
index 0743979..f248a00 100644
--- a/modules/module/settings/hosts.nix
+++ b/modules/module/settings/hosts.nix
@@ -15,7 +15,7 @@
         nvim-host.enable = true;
         nvim-host.package = "${pkgs.neovide}/bin/neovide";
         nvim-host.argv0 = "neovide";
-        nvim-host.flags."--neovim-bin" = "${placeholder "out"}/bin/${config.binName}";
+        nvim-host.flags."--neovim-bin" = "${builtins.placeholder "out"}/bin/${config.binName}";
       };
 
       m = {
diff --git a/modules/module/settings/lang-packages.nix b/modules/module/settings/lang-packages.nix
index 3315363..531b811 100644
--- a/modules/module/settings/lang-packages.nix
+++ b/modules/module/settings/lang-packages.nix
@@ -26,7 +26,7 @@
     };
     default = { };
     description = ''
-      Language-specific package overrides appended to each language spec's extraPackages.
+      Language-specific package overrides appended to each language spec's runtimePackages.
       Intended for flake.nix overrides via wrapper.config.wrap.
     '';
   };
diff --git a/modules/module/settings/runtime-path.nix b/modules/module/settings/runtime-path.nix
index 96c5d0f..b321019 100644
--- a/modules/module/settings/runtime-path.nix
+++ b/modules/module/settings/runtime-path.nix
@@ -10,14 +10,13 @@ let
         let
           is_enabled = if spec ? enable then spec.enable else true;
           has_runtime_deps = (spec.runtimeDeps or false) == runtime_deps_type;
-          packages = spec.extraPackages or [ ];
+          packages = spec.runtimePackages or [ ];
         in
         acc ++ lib.optionals (is_enabled && has_runtime_deps) packages
       )
       [ ];
 
   prefix_packages = collect_runtime_packages "prefix";
-  suffix_packages = collect_runtime_packages "suffix";
 
   to_path_specs = packages: [
     {
@@ -31,5 +30,4 @@ let
 in
 {
   config.prefixVar = lib.optionals (prefix_packages != [ ]) (to_path_specs prefix_packages);
-  config.suffixVar = lib.optionals (suffix_packages != [ ]) (to_path_specs suffix_packages);
 }
diff --git a/modules/module/specs/cats-enable.nix b/modules/module/specs/cats-enable.nix
deleted file mode 100644
index f5a9826..0000000
--- a/modules/module/specs/cats-enable.nix
+++ /dev/null
@@ -1,51 +0,0 @@
-{ config, lib, ... }:
-{
-  # This module implements category-based enabling of specs.
-  # It runs early (order 200) so other specMaps can see the enable flags.
-  #
-  # How it works:
-  # 1. For each spec, extract its name (removing -lazy suffix if present)
-  # 2. Check if there's a corresponding cats.<name> toggle
-  # 3. Set spec.value.enable based on the cats toggle (default: true)
-  # 4. This allows specs to be conditionally included based on config.cats settings
-  #
-  # Example: If config.cats.python = false, then specs.python.enable = false
-
-  config.specMaps = lib.mkOrder 200 [
-    {
-      name = "CATS_ENABLE";
-      data =
-        list:
-        map (
-          v:
-          if v.type == "spec" || v.type == "parent" then
-            let
-              # Extract spec name, handling lazy specs (remove -lazy suffix)
-              specName =
-                if v.name == null then
-                  null
-                else if lib.hasSuffix "-lazy" v.name then
-                  lib.removeSuffix "-lazy" v.name
-                else
-                  v.name;
-
-              # Check if this spec has a corresponding cat toggle
-              catEnabled =
-                if specName != null && builtins.hasAttr specName config.cats then
-                  config.cats.${specName}
-                else
-                  true;  # Default to enabled if no cat toggle exists
-            in
-            v
-            // {
-              value = v.value // {
-                # Use explicit enable if set, otherwise use cat toggle
-                enable = if v.value ? enable then v.value.enable else catEnabled;
-              };
-            }
-          else
-            v
-        ) list;
-    }
-  ];
-}
diff --git a/modules/module/specs/deps.nix b/modules/module/specs/deps.nix
index a8bfaf6..c3a40ea 100644
--- a/modules/module/specs/deps.nix
+++ b/modules/module/specs/deps.nix
@@ -5,24 +5,14 @@
   wlib,
   ...
 }: {
-  # ============================================================================
-  # SPEC MODULE DEFAULTS
-  # ============================================================================
-  # Define default options available to all specs
-
   config.specMods = {parentSpec ? null, ...}: {
-    options.extraPackages = lib.mkOption {
+    options.runtimePkgs = lib.mkOption {
       type = lib.types.listOf wlib.types.stringable;
       default = [];
-      description = "a extraPackages spec field to put packages to suffix to the PATH";
+      description = "a runtimePkgs spec field to put packages to suffix to the PATH";
     };
   };
 
-  # ============================================================================
-  # EXTERNAL TOOLS SPEC
-  # ============================================================================
-  # Core system tools and utilities
-
   config.specs.external = {
     data = lib.mkDefault null;
     before = ["INIT_MAIN"];
@@ -30,7 +20,7 @@
       vim.o.shell = "${pkgs.zsh}/bin/zsh"
     '';
     runtimeDeps = "prefix";
-    extraPackages = with pkgs; [
+    runtimePkgs = with pkgs; [
       perl
       ruby
       shfmt
@@ -39,15 +29,11 @@
     ];
   };
 
-  # ============================================================================
-  # OPTIONAL TOOLS SPEC
-  # ============================================================================
-
   config.specs.optional = lib.mkIf (config.cats.optional or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     before = ["INIT_MAIN"];
-    extraPackages = with pkgs; [
+    runtimePkgs = with pkgs; [
       bat
       broot
       devenv
@@ -76,54 +62,38 @@
     ];
   };
 
-  # ============================================================================
-  # MARKDOWN SPEC
-  # ============================================================================
-
   config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    extraPackages = with pkgs; [
+    runtimePkgs = with pkgs; [
       python313Packages.pylatexenc
       quarto
       zk
     ];
   };
 
-  # ============================================================================
-  # NIX SPEC
-  # ============================================================================
-
   config.specs.nix = lib.mkIf (config.cats.nix or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    extraPackages = with pkgs; [
+    runtimePkgs = with pkgs; [
       alejandra
       nix-doc
       nixd
     ];
   };
 
-  # ============================================================================
-  # LUA SPEC
-  # ============================================================================
-
   config.specs.lua = lib.mkIf (config.cats.lua or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    extraPackages = with pkgs; [
+    runtimePkgs = with pkgs; [
       lua-language-server
     ];
   };
 
-  # ============================================================================
-  # PYTHON SPEC
-  # ============================================================================
-
   config.specs.python = lib.mkIf (config.cats.python or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    extraPackages = let
+    runtimePkgs = let
       python_packages_fn =
         if pkgs ? basePythonPackages
         then ps: pkgs.basePythonPackages ps ++ config.settings.lang_packages.python
@@ -139,14 +109,10 @@
       ];
   };
 
-  # ============================================================================
-  # R SPEC
-  # ============================================================================
-
   config.specs.r = lib.mkIf (config.cats.r or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    extraPackages = let
+    runtimePkgs = let
       r_packages = (pkgs.baseRPackages or []) ++ config.settings.lang_packages.r;
     in
       with pkgs; [
@@ -159,30 +125,22 @@
       ];
   };
 
-  # ============================================================================
-  # JULIA SPEC
-  # ============================================================================
-
   config.specs.julia = lib.mkIf (config.cats.julia or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    extraPackages = let
+    runtimePkgs = let
       julia_with_packages =
         pkgs.julia-bin.withPackages config.settings.lang_packages.julia;
     in [julia_with_packages];
   };
 
-  # ============================================================================
-  # CLICKHOUSE SPEC
-  # ============================================================================
-
   config.specs.clickhouse = lib.mkIf (config.cats.clickhouse or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    extraPackages = with pkgs; [
+    runtimePkgs = with pkgs; [
       clickhouse-lts
     ];
   };
 
-  config.extraPackages = config.specCollect (acc: v: acc ++ (v.extraPackages or [])) [];
+  config.runtimePkgs = config.specCollect (acc: v: acc ++ (v.runtimePkgs or [])) [];
 }
diff --git a/modules/module/specs/plugins.nix b/modules/module/specs/plugins.nix
index 431005d..ff00a72 100644
--- a/modules/module/specs/plugins.nix
+++ b/modules/module/specs/plugins.nix
@@ -4,11 +4,11 @@
   lib,
   ...
 }: {
-  config.specs.gitPlugins = {
+  config.specs.gitPlugins = lib.mkIf (config.cats.gitPlugins or true) {
     data = [];
   };
 
-  config.specs.r = {
+  config.specs.r = lib.mkIf (config.cats.r or true) {
     data = with pkgs.vimPlugins; [
       pkgs.r-nvim
       quarto-nvim
@@ -19,14 +19,14 @@
     ];
   };
 
-  config.specs.markdown-lazy = {
+  config.specs.markdown-lazy = lib.mkIf (config.cats.markdown or true) {
     lazy = true;
     data = [
       config.nvim-lib.neovimPlugins.cmp-pandoc-references
     ];
   };
 
-  config.specs.general = {
+  config.specs.general = lib.mkIf (config.cats.general or true) {
     data = with pkgs.vimPlugins; [
       lze
       lzextras
@@ -79,7 +79,7 @@
     ];
   };
 
-  config.specs.lua = {
+  config.specs.lua = lib.mkIf (config.cats.lua or true) {
     data = with pkgs.vimPlugins; [
       luvit-meta
       {
@@ -89,7 +89,7 @@
     ];
   };
 
-  config.specs.markdown = {
+  config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
     data = with pkgs.vimPlugins; [
       quarto-nvim
       render-markdown-nvim
@@ -104,7 +104,7 @@
     ];
   };
 
-  config.specs.utils = {
+  config.specs.utils = lib.mkIf (config.cats.utils or true) {
     data = with pkgs.vimPlugins; [
       blink-cmp
       nvim-lspconfig
@@ -119,7 +119,7 @@
     ];
   };
 
-  config.specs.treesitterParsers = {
+  config.specs.treesitterParsers = lib.mkIf (config.cats.treesitterParsers or true) {
     data = with pkgs.vimPlugins.nvim-treesitter-parsers; [
       bash
       c
@@ -158,7 +158,7 @@
     ];
   };
 
-  config.specs.utils-lazy = {
+  config.specs.utils-lazy = lib.mkIf (config.cats.utils or true) {
     lazy = true;
     data = with pkgs.vimPlugins; [
       blink-compat
@@ -175,7 +175,7 @@
     ];
   };
 
-  config.specs.gitPlugins-lazy = {
+  config.specs.gitPlugins-lazy = lib.mkIf (config.cats.gitPlugins or true) {
     lazy = true;
     data = [];
   };
diff --git a/modules/neovim.nix b/modules/neovim.nix
index ba0361c..64d2cda 100644
--- a/modules/neovim.nix
+++ b/modules/neovim.nix
@@ -7,16 +7,10 @@ inputs:
   ...
 }:
 {
-  # ============================================================================
-  # IMPORTS
-  # ============================================================================
-  # Import the base neovim wrapper module and all configuration modules
-
   imports = [
     wlib.wrapperModules.neovim
     ./module/specs/deps.nix
     ./module/specs/plugins.nix
-    ./module/specs/cats-enable.nix
     ./module/settings/core.nix
     ./module/settings/cats.nix
     ./module/settings/env.nix
@@ -25,11 +19,6 @@ inputs:
     ./module/settings/runtime-path.nix
   ];
 
-  # ============================================================================
-  # HELPER FUNCTIONS
-  # ============================================================================
-  # Utilities for working with plugin inputs
-
   options.nvim-lib.neovimPlugins = lib.mkOption {
     readOnly = true;
     type = lib.types.attrsOf wlib.types.stringable;
@@ -58,11 +47,6 @@ inputs:
       ];
   };
 
-  # ============================================================================
-  # CONFIGURATION
-  # ============================================================================
-  # Pass cats configuration to neovim and expose metadata
-
   config.settings.cats = config.cats;
   config.info.cats = config.cats;
   config.info.nixCats_config_location = config.settings.config_directory;
diff --git a/overlays/default.nix b/overlays/default.nix
index ebb6518..5a4cc6c 100644
--- a/overlays/default.nix
+++ b/overlays/default.nix
@@ -4,9 +4,8 @@ let
 
   rOverlay = import ./r.nix {inherit inputs;};
   rNvimNixOverlay = inputs.r-nvim-nix.overlays.default;
-  franOverlay = inputs.fran.overlays.default;
-  pythonOverlay = import ./python.nix inputs;
-  pluginsOverlay = import ./plugins.nix inputs;
+  pythonOverlay = import ./python.nix {inherit inputs;};
+  pluginsOverlay = import ./plugins.nix {inherit inputs;};
 
   dependencyOverlays = [
     rOverlay
@@ -15,6 +14,11 @@ let
     pluginsOverlay
   ];
   dependencyOverlay = lib.composeManyExtensions dependencyOverlays;
+
+  # franOverlay provides R-specific tooling (radianWrapper, air-formatter).
+  # It is scoped to rixpkgs (via overlays/r.nix) rather than the global
+  # package set, since it only applies to R package derivations.
+  franOverlay = inputs.fran.overlays.default;
 in
 {
   inherit
@@ -26,20 +30,6 @@ in
     dependencyOverlays
     dependencyOverlay;
 
-  # Named exports for downstream composition.
   default = dependencyOverlay;
   dependencies = dependencyOverlays;
-
-  overlays = {
-    inherit
-      rOverlay
-      rNvimNixOverlay
-      franOverlay
-      pythonOverlay
-      pluginsOverlay
-      dependencyOverlays
-      dependencyOverlay;
-    default = dependencyOverlay;
-    dependencies = dependencyOverlays;
-  };
 }
diff --git a/overlays/r.nix b/overlays/r.nix
index a9961fb..14c02eb 100644
--- a/overlays/r.nix
+++ b/overlays/r.nix
@@ -1,55 +1,15 @@
-# R packages overlay (rix)
-#
-# This overlay provides access to R packages from rstats-on-nix.
-#
-# rstats-on-nix maintains snapshots of CRAN packages built with Nix:
-# - Provides reproducible R package versions
-# - Ensures binary cache availability for faster builds
-# - Maintained by the rstats-on-nix community
-#
-# Available attributes after applying this overlay:
-#   - pkgs.rpkgs: R packages from rstats-on-nix
-#   - pkgs.rpkgs.rPackages: All CRAN packages
-#   - pkgs.rpkgs.quarto: Quarto publishing system
-#   - pkgs.rpkgs.rWrapper: R with package management
-#   - pkgs.rWrapper: R wrapper with standard packages pre-configured
-#   - pkgs.quarto: Quarto with R integration and standard packages
-#
-# Custom R packages and tools (radianWrapper, air-formatter) come from
-# the fran overlay which should be applied separately.
-#
-# To use specific R packages, reference them via:
-#   with pkgs.rpkgs.rPackages; [ package1 package2 ]
-#
-# Update the R snapshot date in flake.nix inputs section:
-#   rixpkgs.url = "github:rstats-on-nix/nixpkgs/YYYY-MM-DD"
 {
   inputs,
   ...
 }: final: prev: let
-  # R packages from rstats-on-nix for the current system
   rpkgs = import inputs.rixpkgs {
     system = prev.stdenv.hostPlatform.system;
     overlays = [inputs.fran.overlays.default];
-  }; # rixpkgs.legacyPackages.${prev.stdenv.hostPlatform.system};
-
-  # nvimcom and rnvimserver are provided by the r-nvim-nix flake overlay
-  # (inputs.r-nvim-nix.overlays.default)
-
-  # Standard R packages used by default in rWrapper and quarto
-  reqPkgs = with rpkgs.rPackages; [
-    #    languageserver
-  ];
+  };
 in {
   inherit rpkgs;
-  baseRPackages = reqPkgs;
-
-  # R wrapper with standard packages
-  rWrapper = rpkgs.rWrapper.override {packages = reqPkgs;};
-
-  # Quarto with R integration
-  quarto = rpkgs.quarto.override {extraRPackages = reqPkgs;};
-
-  # Update helper for rix
+  baseRPackages = [ ];
+  rWrapper = rpkgs.rWrapper.override {packages = [ ];};
+  quarto = rpkgs.quarto.override {extraRPackages = [ ];};
   updateR = import ../scripts/updater.nix {pkgs = final;};
 }

From d23c7f6f51b5730f94628dab6ce43f76fb6048f2 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Thu, 21 May 2026 20:04:45 +1000
Subject: [PATCH 13/28] load packages only if installed

---
 flake.nix                 | 51 +++++++++++++++++++-----------------
 ftplugin/markdown.lua     | 55 +++++++++++++++++++++------------------
 plugin/20_startup.lua     | 36 +++++++++++++------------
 plugin/21_datascience.lua | 32 ++++++++++++-----------
 4 files changed, 92 insertions(+), 82 deletions(-)

diff --git a/flake.nix b/flake.nix
index f84715f..2780328 100644
--- a/flake.nix
+++ b/flake.nix
@@ -39,10 +39,8 @@
     wrappers,
     ...
   } @ inputs: let
-    mkWrapperConfig = pkgs: let
-      def = pkgs.lib.mkDefault;
-    in {
-      cats = pkgs.lib.mapAttrs (_: v: def v) {
+    mkWrapperConfig = pkgs: {
+      cats = {
         clickhouse = false;
         gitPlugins = true;
         julia = false;
@@ -55,22 +53,12 @@
       };
       settings = {
         lang_packages = {
-          python = def (with pkgs.python3Packages; [
-            duckdb
-            polars
-          ]);
-          r = def ((with pkgs.rpkgs.rPackages; [
-            arrow
-            broom
-            data_table
-            janitor
-            languageserver
-            styler
-          ]) ++ [ pkgs.nvimcom ]);
-          julia = def ["DataFramesMeta" "QuackIO"];
+          python = [];
+          r = [];
+          julia = [];
         };
       };
-      binName = def "vv";
+      binName = "vv";
     };
 
     wrapperSettings = pkgs: let
@@ -78,7 +66,7 @@
     in
       wrapper.config.wrap {
         inherit pkgs;
-        inherit (cfg) cats settings binName;
+        inherit (cfg) settings binName;
       };
 
     systems = [
@@ -135,14 +123,29 @@
     devShells = forAllSystems (
       system: let
         pkgs = mkPkgs system;
-        cfg = mkWrapperConfig pkgs;
         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"];
+
         pythonPackages = let
           python_packages_fn =
             if pkgs ? basePythonPackages
-            then ps: pkgs.basePythonPackages ps ++ cfg.settings.lang_packages.python
-            else _: cfg.settings.lang_packages.python;
+            then ps: pkgs.basePythonPackages ps ++ pythonPkgs
+            else _: pythonPkgs;
         in
           with pkgs; [
             (python3.withPackages python_packages_fn)
@@ -153,7 +156,7 @@
           ];
 
         rPackages = let
-          r_packages = (pkgs.baseRPackages or []) ++ cfg.settings.lang_packages.r;
+          r_packages = (pkgs.baseRPackages or []) ++ rPkgs;
         in
           with pkgs; [
             (rWrapper.override {packages = r_packages;})
@@ -167,7 +170,7 @@
           ];
 
         juliaPackages = let
-          julia_with_packages = pkgs.julia-bin.withPackages cfg.settings.lang_packages.julia;
+          julia_with_packages = pkgs.julia-bin.withPackages juliaPkgs;
         in [julia_with_packages];
 
         markdownPackages = with pkgs; [
diff --git a/ftplugin/markdown.lua b/ftplugin/markdown.lua
index b673b60..db316fc 100644
--- a/ftplugin/markdown.lua
+++ b/ftplugin/markdown.lua
@@ -1,32 +1,35 @@
 -- Add the key mappings only for Markdown files in a zk notebook.
-if require("zk.util").notebook_root(vim.fn.expand('%:p')) ~= nil then
-  local map = vim.keymap.set
-  -- Open the link under the caret.
-  map("n", "<CR>", "<Cmd>lua vim.lsp.buf.definition()<CR>", { noremap = true, silent = false, buffer = true })
+local nix = require("config.nix")
+if nix.get_cat("markdown", false) then
+  if require("zk.util").notebook_root(vim.fn.expand('%:p')) ~= nil then
+    local map = vim.keymap.set
+    -- Open the link under the caret.
+    map("n", "<CR>", "<Cmd>lua vim.lsp.buf.definition()<CR>", { noremap = true, silent = false, buffer = true })
 
-  -- Create a new note after asking for its title.
-  -- This overrides the global `<leader>zn` mapping to create the note in the same directory as the current buffer.
-  map("n", "<leader>zhn", "<Cmd>ZkNew { dir = vim.fn.expand('%:p:h'), title = vim.fn.input('Title: ') }<CR>",
-    { noremap = true, silent = false, buffer = true, desc = "Note (here)" })
-  -- Create a new note in the same directory as the current buffer, using the current selection for title.
-  map("v", "<leader>zhnt", ":'<,'>ZkNewFromTitleSelection { dir = vim.fn.expand('%:p:h') }<CR>",
-    { noremap = true, silent = false, buffer = true, desc = "Note from selection (title)" })
-  -- Create a new note in the same directory as the current buffer, using the current selection for note content and asking for its title.
-  map("v", "<leader>zhnc",
-    ":'<,'>ZkNewFromContentSelection { dir = vim.fn.expand('%:p:h'), title = vim.fn.input('Title: ') }<CR>",
-    { noremap = true, silent = false, buffer = true, desc = "Note from selection (content)" })
+    -- Create a new note after asking for its title.
+    -- This overrides the global `<leader>zn` mapping to create the note in the same directory as the current buffer.
+    map("n", "<leader>zhn", "<Cmd>ZkNew { dir = vim.fn.expand('%:p:h'), title = vim.fn.input('Title: ') }<CR>",
+      { noremap = true, silent = false, buffer = true, desc = "Note (here)" })
+    -- Create a new note in the same directory as the current buffer, using the current selection for title.
+    map("v", "<leader>zhnt", ":'<,'>ZkNewFromTitleSelection { dir = vim.fn.expand('%:p:h') }<CR>",
+      { noremap = true, silent = false, buffer = true, desc = "Note from selection (title)" })
+    -- Create a new note in the same directory as the current buffer, using the current selection for note content and asking for its title.
+    map("v", "<leader>zhnc",
+      ":'<,'>ZkNewFromContentSelection { dir = vim.fn.expand('%:p:h'), title = vim.fn.input('Title: ') }<CR>",
+      { noremap = true, silent = false, buffer = true, desc = "Note from selection (content)" })
 
-  -- Open notes linking to the current buffer.
-  map("n", "<leader>zb", "<Cmd>ZkBacklinks<CR>", { noremap = true, silent = false, buffer = true, desc = "Backlinks" })
-  -- Alternative for backlinks using pure LSP and showing the source context.
-  --map('n', '<leader>zb', '<Cmd>lua vim.lsp.buf.references()<CR>', opts)
-  -- Open notes linked by the current buffer.
-  map("n", "<leader>zL", "<Cmd>ZkLinks<CR>", { noremap = true, silent = false, buffer = true, desc = "Links" })
-  map("n", "<leader>zi", "<Cmd>ZkInsertLink<CR>", { noremap = true, silent = false, buffer = true, desc = "Insert link" })
+    -- Open notes linking to the current buffer.
+    map("n", "<leader>zb", "<Cmd>ZkBacklinks<CR>", { noremap = true, silent = false, buffer = true, desc = "Backlinks" })
+    -- Alternative for backlinks using pure LSP and showing the source context.
+    --map('n', '<leader>zb', '<Cmd>lua vim.lsp.buf.references()<CR>', opts)
+    -- Open notes linked by the current buffer.
+    map("n", "<leader>zL", "<Cmd>ZkLinks<CR>", { noremap = true, silent = false, buffer = true, desc = "Links" })
+    map("n", "<leader>zi", "<Cmd>ZkInsertLink<CR>", { noremap = true, silent = false, buffer = true, desc = "Insert link" })
 
-  -- Preview a linked note.
-  -- Open the code actions for a visual selection.
-  map("v", "<leader>za", ":'<,'>lua vim.lsp.buf.range_code_action()<CR>",
-    { noremap = true, silent = false, buffer = true, desc = "Code actions" })
+    -- Preview a linked note.
+    -- Open the code actions for a visual selection.
+    map("v", "<leader>za", ":'<,'>lua vim.lsp.buf.range_code_action()<CR>",
+      { noremap = true, silent = false, buffer = true, desc = "Code actions" })
 
+  end
 end
diff --git a/plugin/20_startup.lua b/plugin/20_startup.lua
index ca18bd8..0404b2c 100644
--- a/plugin/20_startup.lua
+++ b/plugin/20_startup.lua
@@ -390,23 +390,25 @@ end)
 
 -- zk
 now_if_args(function()
-  require("zk").setup({
-    picker = "minipick",
-    lsp = {
-      -- `config` is passed to `vim.lsp.start_client(config)`
-      config = {
-        cmd = { "zk", "lsp" },
-        name = "zk",
-        -- on_attach = ...
-        -- etc, see `:h vim.lsp.start_client()`
-      },
+  if nix.get_cat("markdown", false) then
+    require("zk").setup({
+      picker = "minipick",
+      lsp = {
+        -- `config` is passed to `vim.lsp.start_client(config)`
+        config = {
+          cmd = { "zk", "lsp" },
+          name = "zk",
+          -- on_attach = ...
+          -- etc, see `:h vim.lsp.start_client()`
+        },
 
-      -- automatically attach buffers in a zk notebook that match the given filetypes
-      auto_attach = {
-        enabled = true,
-        filetypes = { "markdown" },
-      },
+        -- automatically attach buffers in a zk notebook that match the given filetypes
+        auto_attach = {
+          enabled = true,
+          filetypes = { "markdown" },
+        },
 
-    },
-  })
+      },
+    })
+  end
 end)
diff --git a/plugin/21_datascience.lua b/plugin/21_datascience.lua
index 62d8f49..70902ca 100644
--- a/plugin/21_datascience.lua
+++ b/plugin/21_datascience.lua
@@ -71,22 +71,24 @@ end)
 now(function()
   vim.treesitter.language.register("markdown", { "quarto", "rmd" })
 
-  vim.api.nvim_create_autocmd("FileType", {
-    pattern = { "quarto" },
-    callback = function()
-      require("otter").activate()
-    end,
-  })
+  if nix.get_cat({"r", "markdown"}, false) then
+    vim.api.nvim_create_autocmd("FileType", {
+      pattern = { "quarto" },
+      callback = function()
+        require("otter").activate()
+      end,
+    })
 
-  require("otter").setup({
-    lsp = {
-      diagnostic_update_events = { "BufWritePost", "InsertLeave" },
-    },
-    buffers = {
-      set_filetype = true,
-      write_to_disk = true,
-    },
-  })
+    require("otter").setup({
+      lsp = {
+        diagnostic_update_events = { "BufWritePost", "InsertLeave" },
+      },
+      buffers = {
+        set_filetype = true,
+        write_to_disk = true,
+      },
+    })
+  end
 end)
 
 later(function()

From 6226a1c9b1a9525aa0cf2ed0a4993a89d062911e Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Thu, 21 May 2026 21:10:30 +1000
Subject: [PATCH 14/28] make lua package loading conditional on cat

---
 plugin/22_languages.lua | 29 ++++++++++++++++-------------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/plugin/22_languages.lua b/plugin/22_languages.lua
index 1983b25..ed4682a 100644
--- a/plugin/22_languages.lua
+++ b/plugin/22_languages.lua
@@ -1,6 +1,7 @@
 local add = Config.add
 local now_if_args = Config.now_if_args
 local later = MiniDeps.later
+local nix = require('config.nix')
 
 if not Config.isNixCats then
   local m_add = MiniDeps.add
@@ -12,19 +13,21 @@ end
 
 -- lua
 later(function()
-  add("luvit-meta")
-  add("lazydev")
-  require("lazydev").setup({
-    library = {
-      -- See the configuration section for more details
-      -- Load luvit types when the `vim.uv` word is found
-      "lua",
-      "mini.nvim",
-      "MiniDeps",
-      { path = "luvit-meta/library", words = { "vim%.uv" } },
-      { path = "${3rd}/luv/library", words = { "vim%.uv" } },
-    },
-  })
+  if nix.get_cat("lua", false) then
+    add("luvit-meta")
+    add("lazydev")
+    require("lazydev").setup({
+      library = {
+        -- See the configuration section for more details
+        -- Load luvit types when the `vim.uv` word is found
+        "lua",
+        "mini.nvim",
+        "MiniDeps",
+        { path = "luvit-meta/library", words = { "vim%.uv" } },
+        { path = "${3rd}/luv/library", words = { "vim%.uv" } },
+      },
+    })
+  end
 end)
 
 -- Markdown

From af6d975129768cce36ac4c46198ab2b3ebaafad3 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Thu, 21 May 2026 21:15:50 +1000
Subject: [PATCH 15/28] make quarto load optional on r or markdown cat

---
 plugin/21_datascience.lua | 32 +++++++++++++++++---------------
 1 file changed, 17 insertions(+), 15 deletions(-)

diff --git a/plugin/21_datascience.lua b/plugin/21_datascience.lua
index 70902ca..2e9f86c 100644
--- a/plugin/21_datascience.lua
+++ b/plugin/21_datascience.lua
@@ -71,7 +71,7 @@ end)
 now(function()
   vim.treesitter.language.register("markdown", { "quarto", "rmd" })
 
-  if nix.get_cat({"r", "markdown"}, false) then
+  if nix.get_cat({ "r", "markdown" }, false) then
     vim.api.nvim_create_autocmd("FileType", {
       pattern = { "quarto" },
       callback = function()
@@ -92,22 +92,24 @@ now(function()
 end)
 
 later(function()
-  require("quarto").setup({
-    lspFeatures = {
-      enabled = true,
-      chunks = "curly",
-      languages = { "r", "python", "julia" },
-      diagnostics = {
+  if nix.get_cat({ "r", "markdown" }, false) then
+    require("quarto").setup({
+      lspFeatures = {
         enabled = true,
-        triggers = { "BufWritePost" },
+        chunks = "curly",
+        languages = { "r", "python", "julia" },
+        diagnostics = {
+          enabled = true,
+          triggers = { "BufWritePost" },
+        },
+        completion = {
+          enabled = true,
+        },
       },
-      completion = {
+      codeRunner = {
         enabled = true,
+        default_method = "slime",
       },
-    },
-    codeRunner = {
-      enabled = true,
-      default_method = "slime",
-    },
-  })
+    })
+  end
 end)

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 16/28] 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 17/28] 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 18/28] 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 19/28] 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 20/28] 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 21/28] 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 22/28] 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 23/28] 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 24/28] 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 25/28] 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 83b70216a980559ecd6823cf3e878f274ea743b7 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Mon, 8 Jun 2026 11:02:45 +0100
Subject: [PATCH 26/28] fixed treesitter

---
 lua/nix_smart_send.lua | 26 +++++++++++++++-----------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/lua/nix_smart_send.lua b/lua/nix_smart_send.lua
index c03af4c..1f82383 100644
--- a/lua/nix_smart_send.lua
+++ b/lua/nix_smart_send.lua
@@ -22,9 +22,11 @@ local COMMENT_TYPES = {
 }
 
 function M.get_current_node()
-  local ts_utils = require('nvim-treesitter.ts_utils')
   local cur_win = vim.api.nvim_get_current_win()
-  return ts_utils.get_node_at_cursor(cur_win, true)
+  return vim.treesitter.get_node({
+    winid = cur_win,
+    ignore_injections = true,
+  })
 end
 
 function M.detect_global_node()
@@ -50,7 +52,6 @@ function M.detect_global_node()
 end
 
 function M.move_to_next_non_empty_line()
-  local ts_utils = require('nvim-treesitter.ts_utils')
   -- Search for the next non-empty line
   local line_num = vim.fn.search("[^;\\s]", "W")
 
@@ -86,25 +87,27 @@ function M.move_to_next_non_empty_line()
     line_content = vim.api.nvim_buf_get_lines(0, line_num - 1, line_num, false)[1]
     first_non_ws = line_content:find("%S") or 1
     vim.api.nvim_win_set_cursor(0, { line_num, first_non_ws - 1 })
-    node = ts_utils.get_node_at_cursor()
+    node = vim.treesitter.get_node()
   end
 
   return true
 end
 
 function M.vselect_node(node)
-  local ts_utils = require('nvim-treesitter.ts_utils')
   if not node then
     return false
   end
 
-  local cur_buf = vim.api.nvim_get_current_buf()
-  ts_utils.update_selection(cur_buf, node, "V")
+  local start_row, _, end_row, _ = node:range()
+
+  vim.api.nvim_win_set_cursor(0, { start_row + 1, 0 })
+  vim.cmd("normal! V")
+  vim.api.nvim_win_set_cursor(0, { end_row + 1, 0 })
+
   return true
 end
 
 function M.select_until_global(global_nodes)
-  local ts_utils = require('nvim-treesitter.ts_utils')
   local root_node = M.detect_global_node()
   if not root_node and global_nodes then
     root_node = global_nodes[1]
@@ -113,7 +116,7 @@ function M.select_until_global(global_nodes)
   -- Use empty table if no global nodes provided
   global_nodes = global_nodes or {}
 
-  local node = ts_utils.get_node_at_cursor()
+  local node = vim.treesitter.get_node()
   if not node then
     -- print("No syntax node found at cursor position")
     return nil
@@ -167,7 +170,6 @@ function M.slime_send_region()
 end
 
 function M.send_repl(global_nodes)
-  local ts_utils = require('nvim-treesitter.ts_utils')
   local cur_node = M.get_current_node()
 
   if not cur_node then
@@ -189,7 +191,9 @@ function M.send_repl(global_nodes)
   M.slime_send_region()
 
   -- Move cursor and continue
-  ts_utils.goto_node(sel_node, true)
+  local _, _, er, ec = sel_node:range()
+  vim.api.nvim_win_set_cursor(0, { er + 1, ec })
+
   M.move_to_next_non_empty_line()
 end
 

From 3cf282e4f8d342021addd743400f11db8d88f811 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Mon, 8 Jun 2026 11:03:05 +0100
Subject: [PATCH 27/28] new font for gui

---
 plugin/00_options.lua | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugin/00_options.lua b/plugin/00_options.lua
index 2b4485b..e824333 100644
--- a/plugin/00_options.lua
+++ b/plugin/00_options.lua
@@ -176,7 +176,7 @@ if vim.g.neovide then
   vim.g.neovide_cursor_short_animation_length = 0
   vim.g.neovide_font_hinting = 'none'
   vim.g.neovide_font_edging = 'subpixelantialias'
-  vim.o.guifont = 'Iosevka Nerd Font,Symbols Nerd Font:h14:#e-subpixelantialias:#h-none'
+  vim.o.guifont = 'JetBrainsMono Nerd Font,Symbols Nerd Font:h14:#e-subpixelantialias:#h-none'
   vim.g.neovide_floating_corner_radius = 0.35
   vim.keymap.set("n", "<leader>nf", "<cmd>NeovideFullscreen<CR>", { desc = "Toggle Neovide Fullscreen" })
 end

From 3ba96f380caf6e994515a76a31c43c2d1265400a Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Mon, 29 Jun 2026 09:59:40 +0200
Subject: [PATCH 28/28] Corrected Rnvim setup

---
 .gitignore     |  1 +
 flake.lock     | 24 ++++++++++++------------
 flake.nix      |  4 ++--
 overlays/r.nix | 13 +++++--------
 4 files changed, 20 insertions(+), 22 deletions(-)

diff --git a/.gitignore b/.gitignore
index e402ff0..6e33f00 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@
 .nvimcom
 .commandcode
 .commandcode/
+.r-*
diff --git a/flake.lock b/flake.lock
index 0b89d7a..21dc5ef 100644
--- a/flake.lock
+++ b/flake.lock
@@ -60,49 +60,49 @@
         "rnvimsrc": "rnvimsrc"
       },
       "locked": {
-        "lastModified": 1779438909,
-        "narHash": "sha256-1lvv0bdvSVyeCIgeZ7Ws7ffbDFurA5LJscS9dRLHzC8=",
+        "lastModified": 1781392459,
+        "narHash": "sha256-9CMG+trBd9AX7cWiGPrMr0eJwuZaql+pj2WVGyT417I=",
         "owner": "dwinkler1",
         "repo": "r_nvim_nix",
-        "rev": "ec17e22ab362a0ddfd6c2e9c5e95d43897a143be",
+        "rev": "03d7872d7702db37ede41f3c6e4d4ce4c129e862",
         "type": "github"
       },
       "original": {
         "owner": "dwinkler1",
-        "ref": "v0.99.4",
+        "ref": "v0.99.5",
         "repo": "r_nvim_nix",
         "type": "github"
       }
     },
     "rixpkgs": {
       "locked": {
-        "lastModified": 1771303851,
-        "narHash": "sha256-tgveHozOJ2D/mi3LxVy/FcmLFDlM5XKZxsNB2XpvzaM=",
+        "lastModified": 1782576256,
+        "narHash": "sha256-KOvpL9DJJmShb64mX9QTjhxHaxE8MizQIqNUAniuJ2E=",
         "owner": "dwinkler1",
         "repo": "rixpkgs",
-        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
+        "rev": "815afc01bc0cc9a2eba80906645bd08f976a4401",
         "type": "github"
       },
       "original": {
         "owner": "dwinkler1",
+        "ref": "nixpkgs",
         "repo": "rixpkgs",
-        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
         "type": "github"
       }
     },
     "rnvimsrc": {
       "flake": false,
       "locked": {
-        "lastModified": 1776905071,
-        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
+        "lastModified": 1780759435,
+        "narHash": "sha256-VxgKMOP1hseQre3cas2dmMXZu4PVyl05INla2OdHTU4=",
         "owner": "R-nvim",
         "repo": "R.nvim",
-        "rev": "582f2af11290ac067e49018db38e12a511325556",
+        "rev": "6ca306191531c3e3d501ee1609c84a5d29059386",
         "type": "github"
       },
       "original": {
         "owner": "R-nvim",
-        "ref": "v0.99.4",
+        "ref": "v0.99.5",
         "repo": "R.nvim",
         "type": "github"
       }
diff --git a/flake.nix b/flake.nix
index ee9c05c..d8c0018 100644
--- a/flake.nix
+++ b/flake.nix
@@ -9,10 +9,10 @@
       url = "github:BirdeeHub/nix-wrapper-modules";
       inputs.nixpkgs.follows = "nixpkgs";
     };
-    rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
+    rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs";
 
     r-nvim-nix = {
-      url = "github:dwinkler1/r_nvim_nix/v0.99.4";
+      url = "github:dwinkler1/r_nvim_nix/v0.99.5";
       inputs = {
         nixpkgs.follows = "rixpkgs";
       };
diff --git a/overlays/r.nix b/overlays/r.nix
index 18f01dd..e736b77 100644
--- a/overlays/r.nix
+++ b/overlays/r.nix
@@ -1,14 +1,11 @@
-{
-  inputs,
-  ...
-}: final: prev: let
+{inputs, ...}: final: prev: let
   rpkgs = import inputs.rixpkgs {
     system = prev.stdenv.hostPlatform.system;
-    overlays = [inputs.fran.overlays.default];
+    overlays = [inputs.fran.overlays.default inputs.r-nvim-nix.overlays.default];
   };
 in {
   inherit rpkgs;
-  baseRPackages = [ ];
-  rWrapper = rpkgs.rWrapper.override {packages = [ ];};
-  quarto = rpkgs.quarto.override {extraRPackages = [ ];};
+  baseRPackages = [rpkgs.nvimcom];
+  rWrapper = rpkgs.rWrapper.override {packages = [];};
+  quarto = rpkgs.quarto.override {extraRPackages = [];};
 }