make quarto load optional on r or markdown cat

- Add languageserver to settings.lang_packages.r
- Enable r_language_server in LSP config (plugin/25_lsp.lua)

.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"))
+}

.commandcode/taste/taste.md

@@ -0,0 +1,9 @@
+# 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/
+

flake.lock

@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1776169885,
+        "lastModified": 1778869304,
-        "narHash": "sha256-l/iNYDZ4bGOAFQY2q8y5OAfBBtrDAaPuRQqWaFHVRXM=",
+        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "4bd9165a9165d7b5e33ae57f3eecbcb28fb231c9",
+        "rev": "d233902339c02a9c334e7e593de68855ad26c4cb",
         "type": "github"
       },
       "original": {
@@ -55,19 +55,43 @@
     "plugins-r": {
       "flake": false,
       "locked": {
-        "lastModified": 1776340770,
+        "lastModified": 1776905071,
-        "narHash": "sha256-o/8UZIc/Bq9dWTjA+MpSR5uMUpE7KHTErk+TwWID8Ww=",
+        "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"
       }
     },
+    "r-nvim-nix": {
+      "inputs": {
+        "nixpkgs": [
+          "rixpkgs"
+        ],
+        "rnvimsrc": [
+          "plugins-r"
+        ]
+      },
+      "locked": {
+        "lastModified": 1778684156,
+        "narHash": "sha256-Z4y1tQfkIsPK4NRxGn668HMDfWxnxNxSJ0CAOOXiIfY=",
+        "owner": "dwinkler1",
+        "repo": "r_nvim_nix",
+        "rev": "2f49dfee27886068e2f49cbd54558ce4cc424c82",
+        "type": "github"
+      },
+      "original": {
+        "owner": "dwinkler1",
+        "repo": "r_nvim_nix",
+        "type": "github"
+      }
+    },
     "rixpkgs": {
       "locked": {
         "lastModified": 1771303851,
@@ -79,8 +103,8 @@
       },
       "original": {
         "owner": "dwinkler1",
-        "ref": "nixpkgs",
         "repo": "rixpkgs",
+        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
         "type": "github"
       }
     },
@@ -90,6 +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"
       }
@@ -101,11 +126,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1776375800,
+        "lastModified": 1779297405,
-        "narHash": "sha256-/SSAR77Brr9fbapsh1cb2K47JXCbvwS1GjM4yyDxle8=",
+        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "f11469ca69068bac13d9e163b2bd268cc06dff57",
+        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
         "type": "github"
       },
       "original": {

flake.nix

@@ -1,16 +1,19 @@
-# 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";
     };
-    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";
@@ -20,7 +23,7 @@
     };
 
     "plugins-r" = {
-      url = "github:R-nvim/R.nvim";
+      url = "github:R-nvim/R.nvim/v0.99.4";
       flake = false;
     };
 
@@ -36,45 +39,34 @@
     wrappers,
     ...
   } @ inputs: let
+    mkWrapperConfig = pkgs: {
+      cats = {
+        clickhouse = false;
+        gitPlugins = true;
+        julia = false;
+        lua = true;
+        markdown = true;
+        nix = true;
+        optional = false;
+        python = false;
+        r = true;
+      };
+      settings = {
+        lang_packages = {
+          python = [];
+          r = [];
+          julia = [];
+        };
+      };
+      binName = "vv";
+    };
+
     wrapperSettings = pkgs: let
-      def = pkgs.lib.mkDefault;
+      cfg = mkWrapperConfig pkgs;
     in
       wrapper.config.wrap {
         inherit pkgs;
-        cats = {
+        inherit (cfg) settings binName;
-          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;
-        };
-
-        settings = {
-          lang_packages = {
-            python = with pkgs.python3Packages; [
-              duckdb
-              polars
-            ];
-
-            r = with pkgs.rpkgs.rPackages; [
-              arrow
-              broom
-              data_table
-              janitor
-              styler
-            ];
-
-            julia = ["DataFramesMeta" "QuackIO"];
-          };
-          colorscheme = def "cyberdream";
-          background = def "dark";
-          wrapRc = def true;
-        };
-        binName = def "vv";
       };
 
     systems = [
@@ -85,54 +77,39 @@
 
     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;
+        config = { allowUnfree = true; };
-        overlays = [dependencyOverlay];
+        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;
+      dependencies = overlayDefs.dependencyOverlay;
-      vv = self.overlays.default;
     };
 
-    wrapperModules = {
+    wrapperModules.default = module;
-      default = module;
+    wrapperConfigs.default = wrapper.config;
-      neovim = self.wrapperModules.default;
-    };
-
-    wrappers = {
-      default = wrapper.config;
-      neovim = self.wrappers.default;
-    };
 
     packages = forAllSystems (
       system: let
         pkgs = mkPkgs system;
-        nvimPkg = wrapperSettings pkgs;
       in {
-        default = nvimPkg;
+        default = wrapperSettings pkgs;
-        vv = nvimPkg;
       }
     );
 
@@ -147,13 +124,79 @@
       system: let
         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"];
+
+        pythonPackages = let
+          python_packages_fn =
+            if pkgs ? basePythonPackages
+            then ps: pkgs.basePythonPackages ps ++ pythonPkgs
+            else _: pythonPkgs;
+        in
+          with pkgs; [
+            (python3.withPackages python_packages_fn)
+            nodejs
+            ruff
+            basedpyright
+            uv
+          ];
+
+        rPackages = let
+          r_packages = (pkgs.baseRPackages or []) ++ rPkgs;
+        in
+          with pkgs; [
+            (rWrapper.override {packages = r_packages;})
+            radianWrapper
+            (quarto.override {extraRPackages = r_packages;})
+            air-formatter
+            yaml-language-server
+            updateR
+            nvimcom
+            rnvimserver
+          ];
+
+        juliaPackages = let
+          julia_with_packages = pkgs.julia-bin.withPackages juliaPkgs;
+        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;
       in {
         default = pkgs.mkShell {
           name = "vShell";
-          packages = [nvimPkg];
+          packages = shellPackages;
-          nativeBuildInputs = with pkgs; [] ++ (pkgs.lib.optionals self.wrappers.default.cats.optional [devenv]);
+          nativeBuildInputs = pkgs.lib.optionals wrapper.config.cats.optional [ pkgs.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"
+          '';
         };
       }
     );
@@ -163,18 +206,11 @@
         pkgs = mkPkgs system;
         nvimPkg = wrapperSettings pkgs;
       in {
-        default = nvimPkg;
+        default = pkgs.runCommand "check-vv" {} ''
-        module-eval = let
-          _ = wrapper.config;
-        in
-          pkgs.runCommand "check-module-eval" {} ''
-            echo "Module evaluation successful" > $out
-          '';
-        package-build = pkgs.runCommand "check-vv" {} ''
           BINARY_PATH="${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
 
@@ -187,6 +223,11 @@
             cat version_output.txt >> $out
           fi
         '';
+        module-eval =
+          let _ = wrapper.config;
+          in pkgs.runCommand "check-module-eval" {} ''
+            echo "Module evaluation successful" > $out
+          '';
       }
     );
 

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 nix = require("config.nix")
-  local map = vim.keymap.set
+if nix.get_cat("markdown", false) then
-  -- Open the link under the caret.
+  if require("zk.util").notebook_root(vim.fn.expand('%:p')) ~= nil then
-  map("n", "<CR>", "<Cmd>lua vim.lsp.buf.definition()<CR>", { noremap = true, silent = false, buffer = true })
+    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.
+    -- 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.
+    -- 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>",
+    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)" })
+      { 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.
+    -- 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>",
+    map("v", "<leader>zhnt", ":'<,'>ZkNewFromTitleSelection { dir = vim.fn.expand('%:p:h') }<CR>",
-    { noremap = true, silent = false, buffer = true, desc = "Note from selection (title)" })
+      { 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.
+    -- 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",
+    map("v", "<leader>zhnc",
-    ":'<,'>ZkNewFromContentSelection { dir = vim.fn.expand('%:p:h'), title = vim.fn.input('Title: ') }<CR>",
+      ":'<,'>ZkNewFromContentSelection { dir = vim.fn.expand('%:p:h'), title = vim.fn.input('Title: ') }<CR>",
-    { noremap = true, silent = false, buffer = true, desc = "Note from selection (content)" })
+      { noremap = true, silent = false, buffer = true, desc = "Note from selection (content)" })
 
-  -- Open notes linking to the current buffer.
+    -- Open notes linking to the current buffer.
-  map("n", "<leader>zb", "<Cmd>ZkBacklinks<CR>", { noremap = true, silent = false, buffer = true, desc = "Backlinks" })
+    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.
+    -- Alternative for backlinks using pure LSP and showing the source context.
-  --map('n', '<leader>zb', '<Cmd>lua vim.lsp.buf.references()<CR>', opts)
+    --map('n', '<leader>zb', '<Cmd>lua vim.lsp.buf.references()<CR>', opts)
-  -- Open notes linked by the current buffer.
+    -- 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>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" })
+    map("n", "<leader>zi", "<Cmd>ZkInsertLink<CR>", { noremap = true, silent = false, buffer = true, desc = "Insert link" })
 
-  -- Preview a linked note.
+    -- Preview a linked note.
-  -- Open the code actions for a visual selection.
+    -- Open the code actions for a visual selection.
-  map("v", "<leader>za", ":'<,'>lua vim.lsp.buf.range_code_action()<CR>",
+    map("v", "<leader>za", ":'<,'>lua vim.lsp.buf.range_code_action()<CR>",
-    { noremap = true, silent = false, buffer = true, desc = "Code actions" })
+      { noremap = true, silent = false, buffer = true, desc = "Code actions" })
 
+  end
 end

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 false;
+    r = lib.mkDefault true;
-    test = lib.mkDefault false;
     treesitterParsers = lib.mkDefault true;
     utils = lib.mkDefault true;
   };

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;

modules/module/settings/env.nix

@@ -7,16 +7,21 @@
   # 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 true) {
+      RNVIM_COMPLDIR = "$PWD/.r-compl";
+      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
+      TMPDIR = "$PWD/.r-tmp";
+    })
   ];
 
   # Environment variables with defaults (can be overridden by user)
   config.envDefault = lib.mkMerge [
-    (lib.mkIf (config.cats.r or false) {
+    (lib.mkIf (config.cats.r or true) {
-      R_LIBS_USER =  "./.Rlibs";
+      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
     })
   ];
 }

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 = {

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.
     '';
   };

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);
 }

modules/module/specs/cats-enable.nix

@@ -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;
-    }
-  ];
-}

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 [])) [];
 }

modules/module/specs/plugins.nix

@@ -3,15 +3,14 @@
   pkgs,
   lib,
   ...
-}:
+}: {
-{
+  config.specs.gitPlugins = lib.mkIf (config.cats.gitPlugins or true) {
-  config.specs.gitPlugins = {
+    data = [];
-    data = [ ];
   };
 
-  config.specs.r = {
+  config.specs.r = lib.mkIf (config.cats.r or true) {
     data = with pkgs.vimPlugins; [
-      config.nvim-lib.neovimPlugins.r
+      pkgs.r-nvim
       quarto-nvim
       {
         data = otter-nvim;
@@ -20,14 +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
@@ -80,7 +79,7 @@
     ];
   };
 
-  config.specs.lua = {
+  config.specs.lua = lib.mkIf (config.cats.lua or true) {
     data = with pkgs.vimPlugins; [
       luvit-meta
       {
@@ -90,7 +89,7 @@
     ];
   };
 
-  config.specs.markdown = {
+  config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
     data = with pkgs.vimPlugins; [
       quarto-nvim
       render-markdown-nvim
@@ -105,20 +104,22 @@
     ];
   };
 
-  config.specs.utils = {
+  config.specs.utils = lib.mkIf (config.cats.utils or true) {
     data = with pkgs.vimPlugins; [
       blink-cmp
       nvim-lspconfig
       nvim-treesitter-context
       nvim-treesitter-textobjects
       {
-        data = pkgs.codecompanion-nvim;
+        data = pkgs.codecompanion-nvim.overrideAttrs (old: {
+          doCheck = false;
+        });
         pname = "codecompanion";
       }
     ];
   };
 
-  config.specs.treesitterParsers = {
+  config.specs.treesitterParsers = lib.mkIf (config.cats.treesitterParsers or true) {
     data = with pkgs.vimPlugins.nvim-treesitter-parsers; [
       bash
       c
@@ -157,7 +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
@@ -174,8 +175,8 @@
     ];
   };
 
-  config.specs.gitPlugins-lazy = {
+  config.specs.gitPlugins-lazy = lib.mkIf (config.cats.gitPlugins or true) {
     lazy = true;
-    data = [ ];
+    data = [];
   };
 }

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;

overlays/default.nix

@@ -3,39 +3,33 @@ let
   lib = nixpkgs.lib;
 
   rOverlay = import ./r.nix {inherit inputs;};
-  franOverlay = inputs.fran.overlays.default;
+  rNvimNixOverlay = inputs.r-nvim-nix.overlays.default;
-  pythonOverlay = import ./python.nix inputs;
+  pythonOverlay = import ./python.nix {inherit inputs;};
-  pluginsOverlay = import ./plugins.nix inputs;
+  pluginsOverlay = import ./plugins.nix {inherit inputs;};
 
   dependencyOverlays = [
     rOverlay
+    rNvimNixOverlay
     pythonOverlay
     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
     rOverlay
+    rNvimNixOverlay
     franOverlay
     pythonOverlay
     pluginsOverlay
     dependencyOverlays
     dependencyOverlay;
 
-  # Named exports for downstream composition.
   default = dependencyOverlay;
   dependencies = dependencyOverlays;
-
-  overlays = {
-    inherit
-      rOverlay
-      franOverlay
-      pythonOverlay
-      pluginsOverlay
-      dependencyOverlays
-      dependencyOverlay;
-    default = dependencyOverlay;
-    dependencies = dependencyOverlays;
-  };
 }

overlays/r.nix

@@ -1,52 +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};
+  };
-
-  # Standard R packages used by default in rWrapper and quarto
-  reqPkgs = with rpkgs.rPackages; [
-    #    languageserver
-  ];
 in {
   inherit rpkgs;
-  baseRPackages = reqPkgs;
+  baseRPackages = [ ];
-
+  rWrapper = rpkgs.rWrapper.override {packages = [ ];};
-  # R wrapper with standard packages
+  quarto = rpkgs.quarto.override {extraRPackages = [ ];};
-  rWrapper = rpkgs.rWrapper.override {packages = reqPkgs;};
-
-  # Quarto with R integration
-  quarto = rpkgs.quarto.override {extraRPackages = reqPkgs;};
-
-  # Update helper for rix
   updateR = import ../scripts/updater.nix {pkgs = final;};
 }

plugin/20_startup.lua

@@ -390,23 +390,25 @@ end)
 
 -- zk
 now_if_args(function()
-  require("zk").setup({
+  if nix.get_cat("markdown", false) then
-    picker = "minipick",
+    require("zk").setup({
-    lsp = {
+      picker = "minipick",
-      -- `config` is passed to `vim.lsp.start_client(config)`
+      lsp = {
-      config = {
+        -- `config` is passed to `vim.lsp.start_client(config)`
-        cmd = { "zk", "lsp" },
+        config = {
-        name = "zk",
+          cmd = { "zk", "lsp" },
-        -- on_attach = ...
+          name = "zk",
-        -- etc, see `:h vim.lsp.start_client()`
+          -- on_attach = ...
-      },
+          -- etc, see `:h vim.lsp.start_client()`
+        },
 
-      -- automatically attach buffers in a zk notebook that match the given filetypes
+        -- automatically attach buffers in a zk notebook that match the given filetypes
-      auto_attach = {
+        auto_attach = {
-        enabled = true,
+          enabled = true,
-        filetypes = { "markdown" },
+          filetypes = { "markdown" },
-      },
+        },
 
-    },
+      },
-  })
+    })
+  end
 end)

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()
@@ -65,41 +71,45 @@ end)
 now(function()
   vim.treesitter.language.register("markdown", { "quarto", "rmd" })
 
-  vim.api.nvim_create_autocmd("FileType", {
+  if nix.get_cat({ "r", "markdown" }, false) then
-    pattern = { "quarto" },
+    vim.api.nvim_create_autocmd("FileType", {
-    callback = function()
+      pattern = { "quarto" },
-      require("otter").activate()
+      callback = function()
-    end,
+        require("otter").activate()
-  })
+      end,
+    })
 
-  require("otter").setup({
+    require("otter").setup({
-    lsp = {
+      lsp = {
-      diagnostic_update_events = { "BufWritePost", "InsertLeave" },
+        diagnostic_update_events = { "BufWritePost", "InsertLeave" },
-    },
+      },
-    buffers = {
+      buffers = {
-      set_filetype = true,
+        set_filetype = true,
-      write_to_disk = true,
+        write_to_disk = true,
-    },
+      },
-  })
+    })
+  end
 end)
 
 later(function()
-  require("quarto").setup({
+  if nix.get_cat({ "r", "markdown" }, false) then
-    lspFeatures = {
+    require("quarto").setup({
-      enabled = true,
+      lspFeatures = {
-      chunks = "curly",
-      languages = { "r", "python", "julia" },
-      diagnostics = {
         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 = {
+  end
-      enabled = true,
-      default_method = "slime",
-    },
-  })
 end)

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")
+  if nix.get_cat("lua", false) then
-  add("lazydev")
+    add("luvit-meta")
-  require("lazydev").setup({
+    add("lazydev")
-    library = {
+    require("lazydev").setup({
-      -- See the configuration section for more details
+      library = {
-      -- Load luvit types when the `vim.uv` word is found
+        -- See the configuration section for more details
-      "lua",
+        -- Load luvit types when the `vim.uv` word is found
-      "mini.nvim",
+        "lua",
-      "MiniDeps",
+        "mini.nvim",
-      { path = "luvit-meta/library", words = { "vim%.uv" } },
+        "MiniDeps",
-      { path = "${3rd}/luv/library", words = { "vim%.uv" } },
+        { path = "luvit-meta/library", words = { "vim%.uv" } },
-    },
+        { path = "${3rd}/luv/library", words = { "vim%.uv" } },
-  })
+      },
+    })
+  end
 end)
 
 -- Markdown

plugin/25_lsp.lua

@@ -15,17 +15,17 @@ now_if_args(function()
     marksman = {
       filetypes = { "markdown", "markdown_inline", "codecompanion" },
     },
-    -- r_language_server = {
+    r_ls = {
-    --   filetypes = { 'r', 'rmd', 'rmarkdown' },
+      filetypes = { 'r', 'rmd', 'rmarkdown' },
-    --   settings = {
+      settings = {
-    --     ['r_language_server'] = {
+        ['r_ls'] = {
-    --       lsp = {
+          lsp = {
-    --         rich_documentation = true,
+            rich_documentation = true,
-    --         enable = true,
+            enable = true,
-    --       },
+          },
-    --     },
+        },
-    --   }
+      }
-    -- },
+    },
     julials = {
       settings = {
         julia = {