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 01/15] 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 02/15] 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 03/15] 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 04/15] 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 05/15] 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 06/15] 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 07/15] 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 08/15] 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 09/15] 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 10/15] 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 11/15] 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 12/15] 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 13/15] 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 14/15] 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 15/15] 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)