.Rprofile

@@ -1,5 +0,0 @@
-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

@@ -1,9 +0,0 @@
-# nix
-- For R.nvim in the Nix wrapper, both RNVIM_COMPLDIR (C server compilation) and a writable R_LIBS_USER directory (nvimcom R package installation) must be configured — fixing only one leaves permission errors in the other. Confidence: 0.65
-- For R.nvim writable directories (RNVIM_COMPLDIR, R_LIBS_USER, TMPDIR), prefer project-local paths (e.g., $PWD/.Rlibs) over global cache paths — the cache approach may let the build succeed but still fail at runtime. Confidence: 0.70
-- Do not use lib.mkDefault on values consumed by lib.optionals or other boolean-checking functions — mkDefault wraps values in a priority set that fails "expected a Boolean" at evaluation time. Use plain booleans for inline conditionals, reserving mkDefault for module options resolved by the merge system. Confidence: 0.70
-
-# Taste (Continuously Learned by [CommandCode][cmd])
-
-[cmd]: https://commandcode.ai/
-

flake.lock

@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1778869304,
-        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
+        "lastModified": 1776169885,
+        "narHash": "sha256-l/iNYDZ4bGOAFQY2q8y5OAfBBtrDAaPuRQqWaFHVRXM=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "d233902339c02a9c334e7e593de68855ad26c4cb",
+        "rev": "4bd9165a9165d7b5e33ae57f3eecbcb28fb231c9",
         "type": "github"
       },
       "original": {
@@ -55,43 +55,19 @@
     "plugins-r": {
       "flake": false,
       "locked": {
-        "lastModified": 1776905071,
-        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
+        "lastModified": 1776340770,
+        "narHash": "sha256-o/8UZIc/Bq9dWTjA+MpSR5uMUpE7KHTErk+TwWID8Ww=",
         "owner": "R-nvim",
         "repo": "R.nvim",
-        "rev": "582f2af11290ac067e49018db38e12a511325556",
+        "rev": "b9cfffeb9b4e484aa9e13f01c0eb80230aada455",
         "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,
@@ -103,8 +79,8 @@
       },
       "original": {
         "owner": "dwinkler1",
+        "ref": "nixpkgs",
         "repo": "rixpkgs",
-        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
         "type": "github"
       }
     },
@@ -114,7 +90,6 @@
         "nixpkgs": "nixpkgs",
         "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
         "plugins-r": "plugins-r",
-        "r-nvim-nix": "r-nvim-nix",
         "rixpkgs": "rixpkgs",
         "wrappers": "wrappers"
       }
@@ -126,11 +101,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1779297405,
-        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
+        "lastModified": 1776375800,
+        "narHash": "sha256-/SSAR77Brr9fbapsh1cb2K47JXCbvwS1GjM4yyDxle8=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
+        "rev": "f11469ca69068bac13d9e163b2bd268cc06dff57",
         "type": "github"
       },
       "original": {

flake.nix

@@ -1,19 +1,16 @@
-# Copyright (c) 2026 Daniel
+# Copyright (c) 2026 BirdeeHub
 # 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/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";
+    rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs";
 
     fran = {
       url = "github:dwinkler1/fran";
@@ -23,7 +20,7 @@
     };
 
     "plugins-r" = {
-      url = "github:R-nvim/R.nvim/v0.99.4";
+      url = "github:R-nvim/R.nvim";
       flake = false;
     };
 
@@ -39,34 +36,45 @@
     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
-      cfg = mkWrapperConfig pkgs;
+      def = pkgs.lib.mkDefault;
     in
       wrapper.config.wrap {
         inherit pkgs;
-        inherit (cfg) settings binName;
+        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;
+        };
+
+        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 = [
@@ -77,39 +85,54 @@
 
     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 = { allowUnfree = true; };
-        overlays = [ overlayDefs.dependencyOverlay ];
+        config = extra_pkg_config;
+        overlays = [dependencyOverlay];
       };
 
-    module = (import ./modules/neovim.nix) inputs;
+    module = nixpkgs.lib.modules.importApply ./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 [
-        overlayDefs.dependencyOverlay
+        dependencyOverlay
         (final: prev: {
           vv = wrapper.config.wrap {pkgs = final;};
         })
       ];
-      dependencies = overlayDefs.dependencyOverlay;
+      dependencies = dependencyOverlay;
+      vv = self.overlays.default;
     };
 
-    wrapperModules.default = module;
-    wrapperConfigs.default = wrapper.config;
+    wrapperModules = {
+      default = module;
+      neovim = self.wrapperModules.default;
+    };
+
+    wrappers = {
+      default = wrapper.config;
+      neovim = self.wrappers.default;
+    };
 
     packages = forAllSystems (
       system: let
         pkgs = mkPkgs system;
+        nvimPkg = wrapperSettings pkgs;
       in {
-        default = wrapperSettings pkgs;
+        default = nvimPkg;
+        vv = nvimPkg;
       }
     );
 
@@ -124,79 +147,13 @@
       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 = shellPackages;
-          nativeBuildInputs = pkgs.lib.optionals wrapper.config.cats.optional [ pkgs.devenv ];
-          shellHook = ''
-            echo 'I am a NixShell'
-            export R_HOME=$(R RHOME)
-            export R_LIBS_SITE=$(strings "$(command -v R)" | grep -oP '/nix/store/[^:]+/library' | sort -u | paste -sd: -)
-            export R_LIBS_USER="$PWD/.r-libs"
-            mkdir -p "$R_LIBS_USER"
-          '';
+          packages = [nvimPkg];
+          nativeBuildInputs = with pkgs; [] ++ (pkgs.lib.optionals self.wrappers.default.cats.optional [devenv]);
+          inputsFrom = [];
+          shellHook = "";
         };
       }
     );
@@ -206,11 +163,18 @@
         pkgs = mkPkgs system;
         nvimPkg = wrapperSettings pkgs;
       in {
-        default = pkgs.runCommand "check-vv" {} ''
+        default = nvimPkg;
+        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 not found or not executable"
+            echo "Error: Binary n not found or not executable"
             exit 1
           fi
 
@@ -223,11 +187,6 @@
             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

@@ -1,7 +1,5 @@
 -- Add the key mappings only for Markdown files in a zk notebook.
-local nix = require("config.nix")
-if nix.get_cat("markdown", false) then
-  if require("zk.util").notebook_root(vim.fn.expand('%:p')) ~= nil 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 })
@@ -31,5 +29,4 @@ if nix.get_cat("markdown", false) then
   map("v", "<leader>za", ":'<,'>lua vim.lsp.buf.range_code_action()<CR>",
     { noremap = true, silent = false, buffer = true, desc = "Code actions" })
 
-  end
 end

modules/module/settings/cats.nix

@@ -14,6 +14,7 @@
 
       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
@@ -24,6 +25,7 @@
       - 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
     '';
@@ -31,16 +33,18 @@
 
   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 true;
+    markdown = lib.mkDefault false;
     nix = lib.mkDefault true;
     optional = lib.mkDefault false;
     python = lib.mkDefault false;
-    r = lib.mkDefault true;
+    r = lib.mkDefault false;
+    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 true) [ lp.tiktoken_core ];
+    lib.optionals (config.cats.general or false) [ 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 = lib.mkDefault false;
+  config.settings.dont_link = false;
 
   # Create additional aliases for the binary
-  config.settings.aliases = lib.mkDefault [ "vvim" ];
+  config.settings.aliases = [ "vvim" ];
 
   # Enable wrapper handling of spec runtimeDeps (template pattern).
   config.settings.autowrapRuntimeDeps = true;

modules/module/settings/env.nix

@@ -7,21 +7,16 @@
   # Environment variables set for the wrapper.
   # These are available when running neovim.
   config.env = lib.mkMerge [
-    (lib.mkIf (config.cats.python or true) {
+    (lib.mkIf (config.cats.python or false) {
       UV_PYTHON_DOWNLOADS = "never";
       UV_PYTHON = pkgs.python.interpreter;
     })
-    (lib.mkIf (config.cats.r or true) {
-      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 true) {
-      R_LIBS_USER = "${pkgs.nvimcom}/library:$PWD/.Rlibs";
+    (lib.mkIf (config.cats.r or false) {
+      R_LIBS_USER =  "./.Rlibs";
     })
   ];
 }

modules/module/settings/hosts.nix

@@ -15,7 +15,7 @@
         nvim-host.enable = true;
         nvim-host.package = "${pkgs.neovide}/bin/neovide";
         nvim-host.argv0 = "neovide";
-        nvim-host.flags."--neovim-bin" = "${builtins.placeholder "out"}/bin/${config.binName}";
+        nvim-host.flags."--neovim-bin" = "${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 runtimePackages.
+      Language-specific package overrides appended to each language spec's extraPackages.
       Intended for flake.nix overrides via wrapper.config.wrap.
     '';
   };

modules/module/settings/runtime-path.nix

@@ -10,13 +10,14 @@ let
         let
           is_enabled = if spec ? enable then spec.enable else true;
           has_runtime_deps = (spec.runtimeDeps or false) == runtime_deps_type;
-          packages = spec.runtimePackages or [ ];
+          packages = spec.extraPackages 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: [
     {
@@ -30,4 +31,5 @@ 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

@@ -0,0 +1,51 @@
+{ 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

@@ -5,14 +5,24 @@
   wlib,
   ...
 }: {
+  # ============================================================================
+  # SPEC MODULE DEFAULTS
+  # ============================================================================
+  # Define default options available to all specs
+
   config.specMods = {parentSpec ? null, ...}: {
-    options.runtimePkgs = lib.mkOption {
+    options.extraPackages = lib.mkOption {
       type = lib.types.listOf wlib.types.stringable;
       default = [];
-      description = "a runtimePkgs spec field to put packages to suffix to the PATH";
+      description = "a extraPackages 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"];
@@ -20,7 +30,7 @@
       vim.o.shell = "${pkgs.zsh}/bin/zsh"
     '';
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
+    extraPackages = with pkgs; [
       perl
       ruby
       shfmt
@@ -29,11 +39,15 @@
     ];
   };
 
+  # ============================================================================
+  # OPTIONAL TOOLS SPEC
+  # ============================================================================
+
   config.specs.optional = lib.mkIf (config.cats.optional or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
     before = ["INIT_MAIN"];
-    runtimePkgs = with pkgs; [
+    extraPackages = with pkgs; [
       bat
       broot
       devenv
@@ -62,38 +76,54 @@
     ];
   };
 
+  # ============================================================================
+  # MARKDOWN SPEC
+  # ============================================================================
+
   config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
+    extraPackages = with pkgs; [
       python313Packages.pylatexenc
       quarto
       zk
     ];
   };
 
+  # ============================================================================
+  # NIX SPEC
+  # ============================================================================
+
   config.specs.nix = lib.mkIf (config.cats.nix or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
+    extraPackages = with pkgs; [
       alejandra
       nix-doc
       nixd
     ];
   };
 
+  # ============================================================================
+  # LUA SPEC
+  # ============================================================================
+
   config.specs.lua = lib.mkIf (config.cats.lua or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = with pkgs; [
+    extraPackages = with pkgs; [
       lua-language-server
     ];
   };
 
+  # ============================================================================
+  # PYTHON SPEC
+  # ============================================================================
+
   config.specs.python = lib.mkIf (config.cats.python or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = let
+    extraPackages = let
       python_packages_fn =
         if pkgs ? basePythonPackages
         then ps: pkgs.basePythonPackages ps ++ config.settings.lang_packages.python
@@ -109,10 +139,14 @@
       ];
   };
 
+  # ============================================================================
+  # R SPEC
+  # ============================================================================
+
   config.specs.r = lib.mkIf (config.cats.r or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = let
+    extraPackages = let
       r_packages = (pkgs.baseRPackages or []) ++ config.settings.lang_packages.r;
     in
       with pkgs; [
@@ -125,22 +159,30 @@
       ];
   };
 
+  # ============================================================================
+  # JULIA SPEC
+  # ============================================================================
+
   config.specs.julia = lib.mkIf (config.cats.julia or true) {
     data = lib.mkDefault null;
     runtimeDeps = "prefix";
-    runtimePkgs = let
+    extraPackages = 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";
-    runtimePkgs = with pkgs; [
+    extraPackages = with pkgs; [
       clickhouse-lts
     ];
   };
 
-  config.runtimePkgs = config.specCollect (acc: v: acc ++ (v.runtimePkgs or [])) [];
+  config.extraPackages = config.specCollect (acc: v: acc ++ (v.extraPackages or [])) [];
 }

modules/module/specs/plugins.nix

@@ -3,14 +3,15 @@
   pkgs,
   lib,
   ...
-}: {
-  config.specs.gitPlugins = lib.mkIf (config.cats.gitPlugins or true) {
-    data = [];
+}:
+{
+  config.specs.gitPlugins = {
+    data = [ ];
   };
 
-  config.specs.r = lib.mkIf (config.cats.r or true) {
+  config.specs.r = {
     data = with pkgs.vimPlugins; [
-      pkgs.r-nvim
+      config.nvim-lib.neovimPlugins.r
       quarto-nvim
       {
         data = otter-nvim;
@@ -19,14 +20,14 @@
     ];
   };
 
-  config.specs.markdown-lazy = lib.mkIf (config.cats.markdown or true) {
+  config.specs.markdown-lazy = {
     lazy = true;
     data = [
       config.nvim-lib.neovimPlugins.cmp-pandoc-references
     ];
   };
 
-  config.specs.general = lib.mkIf (config.cats.general or true) {
+  config.specs.general = {
     data = with pkgs.vimPlugins; [
       lze
       lzextras
@@ -79,7 +80,7 @@
     ];
   };
 
-  config.specs.lua = lib.mkIf (config.cats.lua or true) {
+  config.specs.lua = {
     data = with pkgs.vimPlugins; [
       luvit-meta
       {
@@ -89,7 +90,7 @@
     ];
   };
 
-  config.specs.markdown = lib.mkIf (config.cats.markdown or true) {
+  config.specs.markdown = {
     data = with pkgs.vimPlugins; [
       quarto-nvim
       render-markdown-nvim
@@ -104,22 +105,20 @@
     ];
   };
 
-  config.specs.utils = lib.mkIf (config.cats.utils or true) {
+  config.specs.utils = {
     data = with pkgs.vimPlugins; [
       blink-cmp
       nvim-lspconfig
       nvim-treesitter-context
       nvim-treesitter-textobjects
       {
-        data = pkgs.codecompanion-nvim.overrideAttrs (old: {
-          doCheck = false;
-        });
+        data = pkgs.codecompanion-nvim;
         pname = "codecompanion";
       }
     ];
   };
 
-  config.specs.treesitterParsers = lib.mkIf (config.cats.treesitterParsers or true) {
+  config.specs.treesitterParsers = {
     data = with pkgs.vimPlugins.nvim-treesitter-parsers; [
       bash
       c
@@ -158,7 +157,7 @@
     ];
   };
 
-  config.specs.utils-lazy = lib.mkIf (config.cats.utils or true) {
+  config.specs.utils-lazy = {
     lazy = true;
     data = with pkgs.vimPlugins; [
       blink-compat
@@ -175,8 +174,8 @@
     ];
   };
 
-  config.specs.gitPlugins-lazy = lib.mkIf (config.cats.gitPlugins or true) {
+  config.specs.gitPlugins-lazy = {
     lazy = true;
-    data = [];
+    data = [ ];
   };
 }

modules/neovim.nix

@@ -7,10 +7,16 @@ 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
@@ -19,6 +25,11 @@ 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;
@@ -47,6 +58,11 @@ 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

@@ -3,33 +3,39 @@ let
   lib = nixpkgs.lib;
 
   rOverlay = import ./r.nix {inherit inputs;};
-  rNvimNixOverlay = inputs.r-nvim-nix.overlays.default;
-  pythonOverlay = import ./python.nix {inherit inputs;};
-  pluginsOverlay = import ./plugins.nix {inherit inputs;};
+  franOverlay = inputs.fran.overlays.default;
+  pythonOverlay = import ./python.nix inputs;
+  pluginsOverlay = import ./plugins.nix 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

@@ -1,15 +1,52 @@
+# 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 = [ ];
-  rWrapper = rpkgs.rWrapper.override {packages = [ ];};
-  quarto = rpkgs.quarto.override {extraRPackages = [ ];};
+  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
   updateR = import ../scripts/updater.nix {pkgs = final;};
 }

plugin/20_startup.lua

@@ -390,7 +390,6 @@ end)
 
 -- zk
 now_if_args(function()
-  if nix.get_cat("markdown", false) then
   require("zk").setup({
     picker = "minipick",
     lsp = {
@@ -410,5 +409,4 @@ now_if_args(function()
 
     },
   })
-  end
 end)

plugin/21_datascience.lua

@@ -44,12 +44,6 @@ 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()
@@ -71,7 +65,6 @@ end)
 now(function()
   vim.treesitter.language.register("markdown", { "quarto", "rmd" })
 
-  if nix.get_cat({ "r", "markdown" }, false) then
   vim.api.nvim_create_autocmd("FileType", {
     pattern = { "quarto" },
     callback = function()
@@ -88,11 +81,9 @@ now(function()
       write_to_disk = true,
     },
   })
-  end
 end)
 
 later(function()
-  if nix.get_cat({ "r", "markdown" }, false) then
   require("quarto").setup({
     lspFeatures = {
       enabled = true,
@@ -111,5 +102,4 @@ later(function()
       default_method = "slime",
     },
   })
-  end
 end)

plugin/22_languages.lua

@@ -1,7 +1,6 @@
 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
@@ -13,7 +12,6 @@ end
 
 -- lua
 later(function()
-  if nix.get_cat("lua", false) then
   add("luvit-meta")
   add("lazydev")
   require("lazydev").setup({
@@ -27,7 +25,6 @@ later(function()
       { 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_ls = {
-      filetypes = { 'r', 'rmd', 'rmarkdown' },
-      settings = {
-        ['r_ls'] = {
-          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 = {