From 31bc081831614b9c34b7db920e54ae4556824ef7 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 29 Apr 2026 06:25:26 +0000
Subject: [PATCH 01/14] fix: enable full Quarto support when R is activated

Agent-Logs-Url: https://github.com/dwinkler1/np/sessions/8f21e9a2-22be-44c9-aa37-bc4fd64b20a3

Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>
---
 templates/rde/flake.nix      | 21 ++++++++++++++++++---
 templates/rde/overlays/r.nix |  2 ++
 2 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/templates/rde/flake.nix b/templates/rde/flake.nix
index 12ae4f0..27e3f5a 100644
--- a/templates/rde/flake.nix
+++ b/templates/rde/flake.nix
@@ -185,6 +185,10 @@
                     julia = config.enabledLanguages.julia;
                     python = config.enabledLanguages.python;
                     r = config.enabledLanguages.r;
+                    # Enable markdown/quarto plugins whenever R is active so that
+                    # .qmd buffers get proper syntax highlighting and chunk
+                    # recognition via quarto-nvim and otter-nvim.
+                    markdown = config.enabledLanguages.r;
                     project = true;
                     gitPlugins = config.enabledPackages.gitPlugins;
                     background = config.theme.background;
@@ -202,11 +206,22 @@
     # Development shell configuration
     devShells = forSystems (system: let
       pkgs = import nixpkgs {inherit system;};
+      # When R is enabled, build an overlaid pkgs that includes the R-enhanced
+      # quarto (with knitr and other R packages baked in via extraRPackages).
+      # This ensures `quarto render` from the terminal also works correctly.
+      rPkgs =
+        if config.enabledLanguages.r
+        then
+          import nixpkgs {
+            inherit system;
+            overlays = [rixOverlay rOverlay];
+          }
+        else pkgs;
       # Language-specific packages that should be available in shell
-      languagePackages = with pkgs;
+      languagePackages =
         []
-        ++ (if config.enabledLanguages.r then [quarto] else [])
-        ++ (if config.enabledLanguages.python then [uv] else [])
+        ++ (if config.enabledLanguages.r then [rPkgs.quarto] else [])
+        ++ (if config.enabledLanguages.python then [pkgs.uv] else [])
         ++ (if config.enabledLanguages.julia then [] else []);
     in {
       default = pkgs.mkShell {
diff --git a/templates/rde/overlays/r.nix b/templates/rde/overlays/r.nix
index 255079b..13415ba 100644
--- a/templates/rde/overlays/r.nix
+++ b/templates/rde/overlays/r.nix
@@ -18,8 +18,10 @@ final: prev: let
       broom         # Tidy model outputs
       data_table    # Fast data manipulation
       janitor       # Data cleaning helpers
+      knitr         # Required by Quarto to execute R code chunks
       languageserver # LSP for IDE support
       reprex        # Reproducible examples
+      rmarkdown     # Required by Quarto for R-based rendering
       styler        # Code formatting
       tidyverse     # Data science ecosystem
     ]

From dad9e7d14e5afe57ec820c528aedf16a106339d7 Mon Sep 17 00:00:00 2001
From: Daniel <dw@dwinkler.org>
Date: Sun, 3 May 2026 16:39:21 +1000
Subject: [PATCH 02/14] Remove dependency update command from workflow

Removed the command to update dependencies in the RDE template.
---
 .github/workflows/update.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml
index a42ac30..96cb868 100644
--- a/.github/workflows/update.yml
+++ b/.github/workflows/update.yml
@@ -22,7 +22,6 @@ jobs:
           name: rde
           authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
           extraPullNames: rstats-on-nix, nix-community
-      - run: cd templates/rde/ && nix develop -c p-updateDeps
       - name: Update ed flake.lock
         uses: DeterminateSystems/update-flake-lock@v28
         with:

From c1c92ec37c2d7183be4a0ba575e3d26d74400273 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Sun, 3 May 2026 06:40:30 +0000
Subject: [PATCH 03/14] flake.lock: Update
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Flake lock file updates:

• Updated input 'nixpkgs':
    'github:NixOS/nixpkgs/0726a0ecb6d4e08f6adced58726b95db924cef57?narHash=sha256-EHq1/OX139R1RvBzOJ0aMRT3xnWyqtHBRUBuO1gFzjI%3D' (2026-04-22)
  → 'github:NixOS/nixpkgs/15f4ee454b1dce334612fa6843b3e05cf546efab?narHash=sha256-Ad49moKWeXtKBJNy2ebiTQUEgdLyvGmTeykAQ9xM%2BZ4%3D' (2026-04-30)
• Updated input 'nvimConfig':
    'github:dwinkler1/nvimConfig/2617face3b1be40534d2cae7f0a374a062b3710d?narHash=sha256-pU3u7T4MqpjUWxflNvd4i47FURp756L7nMRL8MV%2BQEw%3D' (2026-04-17)
  → 'github:dwinkler1/nvimConfig/e9c99811d4b8684814608c7bff89dd5bb4d20cda?narHash=sha256-PY%2BhOXV5%2BW0rpWtnUI9QO3tFyyzlpDG8rVjPbaBoHxo%3D' (2026-05-03)
---
 templates/ed/flake.lock | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/templates/ed/flake.lock b/templates/ed/flake.lock
index 8da8614..3457e77 100644
--- a/templates/ed/flake.lock
+++ b/templates/ed/flake.lock
@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1776877367,
-        "narHash": "sha256-EHq1/OX139R1RvBzOJ0aMRT3xnWyqtHBRUBuO1gFzjI=",
+        "lastModified": 1777578337,
+        "narHash": "sha256-Ad49moKWeXtKBJNy2ebiTQUEgdLyvGmTeykAQ9xM+Z4=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "0726a0ecb6d4e08f6adced58726b95db924cef57",
+        "rev": "15f4ee454b1dce334612fa6843b3e05cf546efab",
         "type": "github"
       },
       "original": {
@@ -54,11 +54,11 @@
         "wrappers": "wrappers"
       },
       "locked": {
-        "lastModified": 1776413627,
-        "narHash": "sha256-pU3u7T4MqpjUWxflNvd4i47FURp756L7nMRL8MV+QEw=",
+        "lastModified": 1777790156,
+        "narHash": "sha256-PY+hOXV5+W0rpWtnUI9QO3tFyyzlpDG8rVjPbaBoHxo=",
         "owner": "dwinkler1",
         "repo": "nvimConfig",
-        "rev": "2617face3b1be40534d2cae7f0a374a062b3710d",
+        "rev": "e9c99811d4b8684814608c7bff89dd5bb4d20cda",
         "type": "github"
       },
       "original": {

From 24175e36c3540693f918ee629ac79fbb609342cc Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Thu, 7 May 2026 08:40:44 +0000
Subject: [PATCH 04/14] flake.lock: Update
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Flake lock file updates:

• Updated input 'nixpkgs':
    'github:NixOS/nixpkgs/15f4ee454b1dce334612fa6843b3e05cf546efab?narHash=sha256-Ad49moKWeXtKBJNy2ebiTQUEgdLyvGmTeykAQ9xM%2BZ4%3D' (2026-04-30)
  → 'github:NixOS/nixpkgs/549bd84d6279f9852cae6225e372cc67fb91a4c1?narHash=sha256-hGdgeU2Nk87RAuZyYjyDjFL6LK7dAZN5RE9%2BhrDTkDU%3D' (2026-05-05)
• Updated input 'nvimConfig':
    'github:dwinkler1/nvimConfig/e9c99811d4b8684814608c7bff89dd5bb4d20cda?narHash=sha256-PY%2BhOXV5%2BW0rpWtnUI9QO3tFyyzlpDG8rVjPbaBoHxo%3D' (2026-05-03)
  → 'github:dwinkler1/nvimConfig/4884bf685f157da4f4d60f8e40febeac0b9bf0e9?narHash=sha256-FB8M8D8YzfSe/oL4l6XGJxErq6nRjWSAeJzNXpk2g0E%3D' (2026-05-07)
• Updated input 'nvimConfig/wrappers':
    'github:BirdeeHub/nix-wrapper-modules/f11469ca69068bac13d9e163b2bd268cc06dff57?narHash=sha256-/SSAR77Brr9fbapsh1cb2K47JXCbvwS1GjM4yyDxle8%3D' (2026-04-16)
  → 'github:BirdeeHub/nix-wrapper-modules/dc5184095ad488e937ec308b52c9c0b218959d8b?narHash=sha256-0DS24OW9d9iz%2Bw0LCz6KpS2IpE2z2gHxeBdMZg9xpDY%3D' (2026-05-05)
• Updated input 'rixpkgs':
    'github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e?narHash=sha256-tgveHozOJ2D/mi3LxVy/FcmLFDlM5XKZxsNB2XpvzaM%3D' (2026-02-17)
  → 'github:dwinkler1/rixpkgs/028af91e9161008fce750f3e249afe471a302037?narHash=sha256-K%2BRz%2BpghAmynE83%2Be9svnNYsDgPnbEohrcPb6duG5wM%3D' (2026-05-07)
---
 templates/ed/flake.lock | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/templates/ed/flake.lock b/templates/ed/flake.lock
index 3457e77..572e58d 100644
--- a/templates/ed/flake.lock
+++ b/templates/ed/flake.lock
@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1777578337,
-        "narHash": "sha256-Ad49moKWeXtKBJNy2ebiTQUEgdLyvGmTeykAQ9xM+Z4=",
+        "lastModified": 1777954456,
+        "narHash": "sha256-hGdgeU2Nk87RAuZyYjyDjFL6LK7dAZN5RE9+hrDTkDU=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "15f4ee454b1dce334612fa6843b3e05cf546efab",
+        "rev": "549bd84d6279f9852cae6225e372cc67fb91a4c1",
         "type": "github"
       },
       "original": {
@@ -54,11 +54,11 @@
         "wrappers": "wrappers"
       },
       "locked": {
-        "lastModified": 1777790156,
-        "narHash": "sha256-PY+hOXV5+W0rpWtnUI9QO3tFyyzlpDG8rVjPbaBoHxo=",
+        "lastModified": 1778114917,
+        "narHash": "sha256-FB8M8D8YzfSe/oL4l6XGJxErq6nRjWSAeJzNXpk2g0E=",
         "owner": "dwinkler1",
         "repo": "nvimConfig",
-        "rev": "e9c99811d4b8684814608c7bff89dd5bb4d20cda",
+        "rev": "4884bf685f157da4f4d60f8e40febeac0b9bf0e9",
         "type": "github"
       },
       "original": {
@@ -102,11 +102,11 @@
     },
     "rixpkgs": {
       "locked": {
-        "lastModified": 1771303851,
-        "narHash": "sha256-tgveHozOJ2D/mi3LxVy/FcmLFDlM5XKZxsNB2XpvzaM=",
+        "lastModified": 1778115084,
+        "narHash": "sha256-K+Rz+pghAmynE83+e9svnNYsDgPnbEohrcPb6duG5wM=",
         "owner": "dwinkler1",
         "repo": "rixpkgs",
-        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
+        "rev": "028af91e9161008fce750f3e249afe471a302037",
         "type": "github"
       },
       "original": {
@@ -133,11 +133,11 @@
         ]
       },
       "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": {

From 5c851aecbaf44287d7d9f7de9510d85be439920b Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Thu, 21 May 2026 20:38:02 +1000
Subject: [PATCH 05/14] temp

---
 templates/ed/flake.nix | 26 ++++++++++++--------------
 1 file changed, 12 insertions(+), 14 deletions(-)

diff --git a/templates/ed/flake.nix b/templates/ed/flake.nix
index 08a618d..7ac16f6 100644
--- a/templates/ed/flake.nix
+++ b/templates/ed/flake.nix
@@ -17,7 +17,7 @@
         nix = true;
         optional = false;
         python = false;
-        r = false;
+        r = true;
       };
 
       settings = let
@@ -69,7 +69,6 @@
 
       env = {
         IS_PROJECT_EDITOR = "1";
-        R_LIBS_USER = "./.nvimcom";
       };
 
       extraPackages = with pkgs; [
@@ -93,14 +92,18 @@
     forAllSystems = nixpkgs.lib.genAttrs systems;
     overlays = [inputs.nvimConfig.overlays.dependencies];
   in {
+    formatter = forAllSystems (system: nixpkgs.legacyPackages.${system}.nixfmt-rfc-style);
+
     packages = forAllSystems (system: let
       pkgs = import nixpkgs {inherit system overlays;};
-      baseNvim = nvimConfig.packages.${system}.default;
-
-      nvim = (baseNvim.eval (projectSettings {inherit pkgs;})).config.wrapper;
-      default = nvim;
+      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
+        modules = [
+          nvimConfig.wrapperModules.default
+          projectSettings
+        ];
+      };
     in {
-      default = nvim;
+      default = evalResult.config.wrap { inherit pkgs; };
     });
 
     devShells = forAllSystems (system: let
@@ -108,14 +111,14 @@
       nv = self.packages.${system}.default;
     in {
       default = pkgs.mkShell {
-        packages = [nv pkgs.updateR];
+        packages = [nv];
       };
     });
   };
 
   inputs = {
     nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
-    rixpkgs.url = "github:dwinkler1/rixpkgs/nixpkgs";
+    rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
     fran = {
       url = "github:dwinkler1/fran";
       inputs = {
@@ -128,12 +131,7 @@
         rixpkgs.follows = "rixpkgs";
         nixpkgs.follows = "nixpkgs";
         fran.follows = "fran";
-        "plugins-r".follows = "plugins-r";
       };
     };
-    "plugins-r" = {
-      url = "github:R-nvim/R.nvim/v0.99.3";
-      flake = false;
-    };
   };
 }

From e814d2c04c36a5542c11caadbcae5148aaf05594 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Thu, 21 May 2026 21:43:04 +1000
Subject: [PATCH 06/14] simplified

---
 templates/ed/README.md  |  73 +++++++++++++
 templates/ed/flake.lock |  65 ++++++++----
 templates/ed/flake.nix  | 223 +++++++++++++++++++++++++---------------
 3 files changed, 256 insertions(+), 105 deletions(-)
 create mode 100644 templates/ed/README.md

diff --git a/templates/ed/README.md b/templates/ed/README.md
new file mode 100644
index 0000000..272d827
--- /dev/null
+++ b/templates/ed/README.md
@@ -0,0 +1,73 @@
+# Project Editor
+
+A per-project Neovim wrapper built with [nix-wrapper-modules](https://birdeehub.github.io/nix-wrapper-modules/) and [nvimConfig](https://github.com/dwinkler1/nvimConfig).
+
+## Setup
+
+The flake provides two entry points:
+
+| Command | What you get |
+|---|---|
+| `direnv allow` / `nix develop` | **(Recommended)** A shell with `nv` and all enabled language toolchains (R, Python, Julia, Quarto) on `PATH`. |
+| `nix run` | Launches only the `nv` editor. Language toolchains (R, Python, etc.) are **not** on `PATH`. |
+
+### With direnv (recommended)
+
+```bash
+direnv allow   # enter the devShell automatically
+nv             # launch the pre-configured Neovim
+R              # R REPL is available (if enabled in flake.nix)
+```
+
+### Without direnv
+
+```bash
+nix develop    # enter the devShell manually
+nv             # launch Neovim
+R              # R REPL is available (if enabled in flake.nix)
+```
+
+> **Why `nix run` only gives the editor:** The flake's `packages.default` is the wrapped Neovim binary. Language toolchains (R, radian, quarto, etc.) live in `devShells.default`. Use `nix develop` (or `direnv allow`) to get the full environment.
+
+## Configuration
+
+The `flake.nix` is the single source of truth. Key knobs:
+
+| Option | What it controls |
+|---|---|
+| `cats` | Toggle language support (nix, r, python, julia, etc.) |
+| `settings.lang_packages.<lang>` | Language-specific packages installed in the wrapper |
+| `settings.colorscheme` | Neovim colorscheme |
+| `settings.background` | `"dark"` or `"light"` |
+| `settings.wrapRc` | When `true`, init.lua is embedded (rebuild to change); when `false`, init.lua is external (reload without rebuild) |
+| `binName` | The wrapper binary name (`nv` by default) |
+| `env` | Environment variables set in the wrapper |
+| `extraPackages` | Extra system packages available in the wrapper's PATH |
+| `specs.extraLua` | Inject lazy.nvim plugin specs |
+
+### Adding packages without editing flake.nix
+
+Create any of these optional files in the project root to add dependencies without modifying `flake.nix`:
+
+- **`python-packages.nix`** — receives `python3Packages`, return a list of packages:
+  ```nix
+  p: with p; [ numpy scipy ]
+  ```
+
+- **`r-packages.nix`** — receives `rpkgs` (includes `rPackages`), return a list:
+  ```nix
+  p: with p.rPackages; [ ggplot2 data.table ]
+  ```
+
+- **`julia-packages.nix`** — no arguments, return a list of package name strings:
+  ```nix
+  [ "DataFrames" "Plots" ]
+  ```
+
+## Formatting
+
+```bash
+nix fmt
+```
+
+Uses `nixfmt-rfc-style` pinned via the flake's `formatter` output.
diff --git a/templates/ed/flake.lock b/templates/ed/flake.lock
index 572e58d..19c77b2 100644
--- a/templates/ed/flake.lock
+++ b/templates/ed/flake.lock
@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1777954456,
-        "narHash": "sha256-hGdgeU2Nk87RAuZyYjyDjFL6LK7dAZN5RE9+hrDTkDU=",
+        "lastModified": 1778869304,
+        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "549bd84d6279f9852cae6225e372cc67fb91a4c1",
+        "rev": "d233902339c02a9c334e7e593de68855ad26c4cb",
         "type": "github"
       },
       "original": {
@@ -45,20 +45,19 @@
           "nixpkgs"
         ],
         "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
-        "plugins-r": [
-          "plugins-r"
-        ],
+        "plugins-r": "plugins-r",
+        "r-nvim-nix": "r-nvim-nix",
         "rixpkgs": [
           "rixpkgs"
         ],
         "wrappers": "wrappers"
       },
       "locked": {
-        "lastModified": 1778114917,
-        "narHash": "sha256-FB8M8D8YzfSe/oL4l6XGJxErq6nRjWSAeJzNXpk2g0E=",
+        "lastModified": 1779362150,
+        "narHash": "sha256-y3JTpxmNgtEYG1m21Ymvdmrul/WvJzOCX45AlV21aak=",
         "owner": "dwinkler1",
         "repo": "nvimConfig",
-        "rev": "4884bf685f157da4f4d60f8e40febeac0b9bf0e9",
+        "rev": "af6d975129768cce36ac4c46198ab2b3ebaafad3",
         "type": "github"
       },
       "original": {
@@ -86,33 +85,58 @@
     "plugins-r": {
       "flake": false,
       "locked": {
-        "lastModified": 1769881528,
-        "narHash": "sha256-oQSHHu6filJkAyH94yEvyTVuxA+5MU2dMOEAnsIjJKQ=",
+        "lastModified": 1776905071,
+        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
         "owner": "R-nvim",
         "repo": "R.nvim",
-        "rev": "958b472d763cb258927c7ef69af4fd9945cc5469",
+        "rev": "582f2af11290ac067e49018db38e12a511325556",
         "type": "github"
       },
       "original": {
         "owner": "R-nvim",
-        "ref": "v0.99.3",
+        "ref": "v0.99.4",
         "repo": "R.nvim",
         "type": "github"
       }
     },
+    "r-nvim-nix": {
+      "inputs": {
+        "nixpkgs": [
+          "nvimConfig",
+          "rixpkgs"
+        ],
+        "rnvimsrc": [
+          "nvimConfig",
+          "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": 1778115084,
-        "narHash": "sha256-K+Rz+pghAmynE83+e9svnNYsDgPnbEohrcPb6duG5wM=",
+        "lastModified": 1771303851,
+        "narHash": "sha256-tgveHozOJ2D/mi3LxVy/FcmLFDlM5XKZxsNB2XpvzaM=",
         "owner": "dwinkler1",
         "repo": "rixpkgs",
-        "rev": "028af91e9161008fce750f3e249afe471a302037",
+        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
         "type": "github"
       },
       "original": {
         "owner": "dwinkler1",
-        "ref": "nixpkgs",
         "repo": "rixpkgs",
+        "rev": "af2dd3f7b4b172077747c0869d4e30702fb71b0e",
         "type": "github"
       }
     },
@@ -121,7 +145,6 @@
         "fran": "fran",
         "nixpkgs": "nixpkgs",
         "nvimConfig": "nvimConfig",
-        "plugins-r": "plugins-r",
         "rixpkgs": "rixpkgs"
       }
     },
@@ -133,11 +156,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1777991014,
-        "narHash": "sha256-0DS24OW9d9iz+w0LCz6KpS2IpE2z2gHxeBdMZg9xpDY=",
+        "lastModified": 1779297405,
+        "narHash": "sha256-VFoBwH7ZjVxCnvZTb5ODRXt70sLtWMxstive0N+RS50=",
         "owner": "BirdeeHub",
         "repo": "nix-wrapper-modules",
-        "rev": "dc5184095ad488e937ec308b52c9c0b218959d8b",
+        "rev": "e7ed7a1205945befdf2e0d73ba7df91d935e5af1",
         "type": "github"
       },
       "original": {
diff --git a/templates/ed/flake.nix b/templates/ed/flake.nix
index 7ac16f6..bc5f7d3 100644
--- a/templates/ed/flake.nix
+++ b/templates/ed/flake.nix
@@ -7,95 +7,107 @@
     nvimConfig,
     ...
   } @ inputs: let
-    projectSettings = {pkgs}: {
-      cats = {
-        clickhouse = false;
-        gitPlugins = false;
-        julia = false;
-        lua = false;
-        markdown = false;
-        nix = true;
-        optional = false;
-        python = false;
-        r = true;
-      };
-
-      settings = let
-        # With `replace` packages are replaced otherwise they are merged with base packages
-        replace = pkgs.lib.mkForce;
-      in {
-        lang_packages = {
-          python = replace (
-            (with pkgs.python3Packages; [
-              duckdb
-              polars
-            ])
-            ++ (
-              if builtins.pathExists ./python-packages.nix
-              # p: with p; [ ... ]
-              then import ./python-packages.nix pkgs.python3Packages
-              else []
-            )
-          );
-
-          r = replace (
-            (with pkgs.rpkgs.rPackages; [
-              fixest
-              # pkgs.extraRPackages.musicMetadata
-            ])
-            ++ (
-              if builtins.pathExists ./r-packages.nix
-              # p: with p.rPackages; [ ... ]
-              then import ./r-packages.nix pkgs.rpkgs
-              else []
-            )
-          );
-
-          julia = replace ([
-              "StatsBase"
-            ]
-            ++ (
-              if builtins.pathExists ./julia-packages.nix
-              # [ ... ]
-              then import ./julia-packages.nix
-              else []
-            ));
-        };
-        colorscheme = "kanagawa";
-        background = "dark";
-        wrapRc = true;
-      };
-      binName = "vv";
-
-      env = {
-        IS_PROJECT_EDITOR = "1";
-      };
-
-      extraPackages = with pkgs; [
-        cowsay
-      ];
-
-      specs.extraLua = let
-        name = builtins.baseNameOf (builtins.toString ./.);
-      in {
-        data = pkgs.vimPlugins.mini-notify;
-        before = ["INIT_MAIN"];
-        config = ''
-          require("mini.notify").setup()
-          vim.notify = MiniNotify.make_notify()
-          vim.notify("Welcome to ${name}!")
-        '';
-      };
+    # ── Shared language support flags ──────────────────────────────
+    # Used by both the neovim wrapper module and the devShell
+    cats = {
+      clickhouse = false;
+      gitPlugins = false;
+      julia = false;
+      lua = false;
+      markdown = false;
+      nix = true;
+      optional = false;
+      python = false;
+      r = false;
     };
 
-    systems = nixpkgs.lib.systems.flakeExposed;
+    # ── Language package lists ────────────────────────────────────
+    # Shared between wrapper lang_packages and devShell toolchains.
+    # Accept pkgs so they work inside forAllSystems for each system.
+
+    rPackages = pkgs:
+      (with pkgs.rpkgs.rPackages; [
+        fixest
+        # pkgs.extraRPackages.musicMetadata
+      ])
+      ++ (
+        if builtins.pathExists ./r-packages.nix
+        # p: with p.rPackages; [ ... ]
+        then import ./r-packages.nix pkgs.rpkgs
+        else []
+      );
+
+    pythonPackages = pkgs:
+      (with pkgs.python3Packages; [
+        duckdb
+        polars
+      ])
+      ++ (
+        if builtins.pathExists ./python-packages.nix
+        # p: with p; [ ... ]
+        then import ./python-packages.nix pkgs.python3Packages
+        else []
+      );
+
+    juliaPackages =
+      ["StatsBase"]
+      ++ (
+        if builtins.pathExists ./julia-packages.nix
+        # [ ... ]
+        then import ./julia-packages.nix
+        else []
+      );
+
+    systems = ["aarch64-darwin" "x86_64-linux" "aarch64-linux"];
     forAllSystems = nixpkgs.lib.genAttrs systems;
     overlays = [inputs.nvimConfig.overlays.dependencies];
   in {
     formatter = forAllSystems (system: nixpkgs.legacyPackages.${system}.nixfmt-rfc-style);
 
     packages = forAllSystems (system: let
-      pkgs = import nixpkgs {inherit system overlays;};
+      pkgs = import nixpkgs {
+        inherit system overlays;
+        config = {allowUnfree = true;};
+      };
+      # Plain attrset — pkgs is captured from the surrounding scope,
+      # so the module system does not need lazy _module.args resolution.
+      projectSettings = {
+        inherit cats;
+        settings = let
+          # With `replace` packages are replaced otherwise they are merged with base packages
+          replace = pkgs.lib.mkForce;
+        in {
+          lang_packages = {
+            python = replace (pythonPackages pkgs);
+            r = replace (rPackages pkgs);
+            julia = replace juliaPackages;
+          };
+          colorscheme = "kanagawa";
+          background = "dark";
+          wrapRc = true;
+        };
+        binName = "nv";
+
+        env = {
+          IS_PROJECT_EDITOR = "1";
+        };
+
+        runtimePkgs = with pkgs; [
+          cowsay
+        ];
+
+        specs.extraLua = let
+          name = builtins.baseNameOf (builtins.toString ./.);
+        in {
+          data = pkgs.vimPlugins.mini-notify;
+          before = ["INIT_MAIN"];
+          config = ''
+            require("mini.notify").setup()
+            vim.notify = MiniNotify.make_notify()
+            vim.notify("Welcome to ${name}!")
+          '';
+        };
+      };
       evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
         modules = [
           nvimConfig.wrapperModules.default
@@ -103,15 +115,58 @@
         ];
       };
     in {
-      default = evalResult.config.wrap { inherit pkgs; };
+      default = evalResult.config.wrap {inherit pkgs;};
     });
 
     devShells = forAllSystems (system: let
-      pkgs = import nixpkgs {inherit system overlays;};
+      pkgs = import nixpkgs {
+        inherit system overlays;
+        config = {allowUnfree = true;};
+      };
       nv = self.packages.${system}.default;
     in {
       default = pkgs.mkShell {
-        packages = [nv];
+        packages =
+          [nv]
+
+          # ── R toolchain (R REPL, quarto, LSP, formatter) ─────
+          ++ pkgs.lib.optionals cats.r (let
+            r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
+          in [
+            (pkgs.rWrapper.override {packages = r_packages;})
+            pkgs.radianWrapper
+            pkgs.air-formatter
+            pkgs.yaml-language-server
+            pkgs.nvimcom
+            pkgs.rnvimserver
+          ])
+
+          # ── Python toolchain (interpreter, LSP, formatter) ────
+          ++ pkgs.lib.optionals cats.python [
+            (pkgs.python3.withPackages (ps: pkgs.basePythonPackages ps ++ pythonPackages pkgs))
+            pkgs.nodejs
+            pkgs.ruff
+            pkgs.basedpyright
+            pkgs.uv
+          ]
+
+          # ── Julia toolchain ───────────────────────────────────
+          ++ pkgs.lib.optionals cats.julia [
+            pkgs.julia-bin.withPackages juliaPackages
+          ]
+
+          # ── Markdown toolchain (quarto, zk) ───────────────────
+          ++ (let
+            r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
+            quarto =
+              if cats.r
+              then pkgs.quarto.override {extraRPackages = r_packages;}
+              else pkgs.quarto;
+          in pkgs.lib.optionals cats.markdown [
+            pkgs.python313Packages.pylatexenc
+            quarto
+            pkgs.zk
+          ]);
       };
     });
   };

From 5d8c198afaffc99a119cfc69256f6bdb99632959 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sat, 23 May 2026 02:27:20 +1000
Subject: [PATCH 07/14] More robust shell setup with nu

---
 templates/ed/flake.nix | 33 ++++++++++++++++++++++-----------
 1 file changed, 22 insertions(+), 11 deletions(-)

diff --git a/templates/ed/flake.nix b/templates/ed/flake.nix
index bc5f7d3..b674c62 100644
--- a/templates/ed/flake.nix
+++ b/templates/ed/flake.nix
@@ -126,9 +126,21 @@
       nv = self.packages.${system}.default;
     in {
       default = pkgs.mkShell {
+        shellHook = ''
+          exec nu
+          alias gst='git status'
+          alias glol='git log --oneline --graph --decorate'
+          alias gc='git commit'
+          alias gl='git pull'
+          alias gp='git push'
+        '';
         packages =
-          [nv]
-
+          [
+            nv
+            pkgs.git
+            pkgs.pre-commit
+            pkgs.nushell
+          ]
           # ── R toolchain (R REPL, quarto, LSP, formatter) ─────
           ++ pkgs.lib.optionals cats.r (let
             r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
@@ -140,7 +152,6 @@
             pkgs.nvimcom
             pkgs.rnvimserver
           ])
-
           # ── Python toolchain (interpreter, LSP, formatter) ────
           ++ pkgs.lib.optionals cats.python [
             (pkgs.python3.withPackages (ps: pkgs.basePythonPackages ps ++ pythonPackages pkgs))
@@ -149,12 +160,11 @@
             pkgs.basedpyright
             pkgs.uv
           ]
-
           # ── Julia toolchain ───────────────────────────────────
           ++ pkgs.lib.optionals cats.julia [
-            pkgs.julia-bin.withPackages juliaPackages
+            pkgs.julia-bin.withPackages
+            juliaPackages
           ]
-
           # ── Markdown toolchain (quarto, zk) ───────────────────
           ++ (let
             r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
@@ -162,11 +172,12 @@
               if cats.r
               then pkgs.quarto.override {extraRPackages = r_packages;}
               else pkgs.quarto;
-          in pkgs.lib.optionals cats.markdown [
-            pkgs.python313Packages.pylatexenc
-            quarto
-            pkgs.zk
-          ]);
+          in
+            pkgs.lib.optionals cats.markdown [
+              pkgs.python313Packages.pylatexenc
+              quarto
+              pkgs.zk
+            ]);
       };
     });
   };

From f844bdff2fabf0ffdd9558c9c9b67cb52aa1eca4 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sat, 23 May 2026 19:58:10 +1000
Subject: [PATCH 08/14] refactor for better runtime dep management

---
 templates/ed/.gitignore |   1 +
 templates/ed/flake.nix  | 127 ++++++++++++++++++++++++++--------------
 2 files changed, 83 insertions(+), 45 deletions(-)

diff --git a/templates/ed/.gitignore b/templates/ed/.gitignore
index 52e8a70..ffc0e1a 100644
--- a/templates/ed/.gitignore
+++ b/templates/ed/.gitignore
@@ -1 +1,2 @@
 .nvimcom
+.commandcode/
diff --git a/templates/ed/flake.nix b/templates/ed/flake.nix
index b674c62..2dbe4db 100644
--- a/templates/ed/flake.nix
+++ b/templates/ed/flake.nix
@@ -28,7 +28,6 @@
     rPackages = pkgs:
       (with pkgs.rpkgs.rPackages; [
         fixest
-        # pkgs.extraRPackages.musicMetadata
       ])
       ++ (
         if builtins.pathExists ./r-packages.nix
@@ -58,11 +57,89 @@
         else []
       );
 
+    # ── Per-language runtime dependencies ──────────────────────────
+    # Single source of truth for system/toolchain packages that
+    # flow to both runtimePkgs (wrapper PATH) and devShells.
+    mkRuntimeDeps = pkgs: {
+      always = [
+        pkgs.git
+        pkgs.pre-commit
+        pkgs.cowsay
+      ];
+      nix = [
+        pkgs.nil
+        pkgs.nixfmt
+      ];
+      r = let
+        r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
+      in [
+        (pkgs.rWrapper.override {packages = r_packages;})
+        pkgs.radianWrapper
+        pkgs.air-formatter
+        pkgs.yaml-language-server
+        pkgs.nvimcom
+        pkgs.rnvimserver
+      ];
+      python = [
+        (pkgs.python3.withPackages (ps:
+          (pkgs.basePythonPackages or (_: [])) ps
+          ++ pythonPackages pkgs))
+        pkgs.nodejs
+        pkgs.ruff
+        pkgs.basedpyright
+        pkgs.uv
+      ];
+      julia = [
+        (pkgs.julia-bin.withPackages juliaPackages)
+      ];
+      markdown = let
+        r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
+        quarto =
+          if cats.r
+          then pkgs.quarto.override {extraRPackages = r_packages;}
+          else pkgs.quarto;
+      in [
+        pkgs.python313Packages.pylatexenc
+        quarto
+        pkgs.zk
+      ];
+    };
+
+    enabledRuntimeDeps = pkgs: let
+      deps = mkRuntimeDeps pkgs;
+    in
+      deps.always
+      ++ (
+        if cats.nix
+        then deps.nix
+        else []
+      )
+      ++ (
+        if cats.r
+        then deps.r
+        else []
+      )
+      ++ (
+        if cats.python
+        then deps.python
+        else []
+      )
+      ++ (
+        if cats.julia
+        then deps.julia
+        else []
+      )
+      ++ (
+        if cats.markdown
+        then deps.markdown
+        else []
+      );
+
     systems = ["aarch64-darwin" "x86_64-linux" "aarch64-linux"];
     forAllSystems = nixpkgs.lib.genAttrs systems;
     overlays = [inputs.nvimConfig.overlays.dependencies];
   in {
-    formatter = forAllSystems (system: nixpkgs.legacyPackages.${system}.nixfmt-rfc-style);
+    formatter = forAllSystems (system: nixpkgs.legacyPackages.${system}.nixfmt);
 
     packages = forAllSystems (system: let
       pkgs = import nixpkgs {
@@ -92,12 +169,10 @@
           IS_PROJECT_EDITOR = "1";
         };
 
-        runtimePkgs = with pkgs; [
-          cowsay
-        ];
+        runtimePkgs = enabledRuntimeDeps pkgs;
 
         specs.extraLua = let
-          name = builtins.baseNameOf (builtins.toString ./.);
+          name = builtins.baseNameOf (builtins.toString "${self.outPath}");
         in {
           data = pkgs.vimPlugins.mini-notify;
           before = ["INIT_MAIN"];
@@ -137,47 +212,9 @@
         packages =
           [
             nv
-            pkgs.git
-            pkgs.pre-commit
             pkgs.nushell
           ]
-          # ── R toolchain (R REPL, quarto, LSP, formatter) ─────
-          ++ pkgs.lib.optionals cats.r (let
-            r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
-          in [
-            (pkgs.rWrapper.override {packages = r_packages;})
-            pkgs.radianWrapper
-            pkgs.air-formatter
-            pkgs.yaml-language-server
-            pkgs.nvimcom
-            pkgs.rnvimserver
-          ])
-          # ── Python toolchain (interpreter, LSP, formatter) ────
-          ++ pkgs.lib.optionals cats.python [
-            (pkgs.python3.withPackages (ps: pkgs.basePythonPackages ps ++ pythonPackages pkgs))
-            pkgs.nodejs
-            pkgs.ruff
-            pkgs.basedpyright
-            pkgs.uv
-          ]
-          # ── Julia toolchain ───────────────────────────────────
-          ++ pkgs.lib.optionals cats.julia [
-            pkgs.julia-bin.withPackages
-            juliaPackages
-          ]
-          # ── Markdown toolchain (quarto, zk) ───────────────────
-          ++ (let
-            r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
-            quarto =
-              if cats.r
-              then pkgs.quarto.override {extraRPackages = r_packages;}
-              else pkgs.quarto;
-          in
-            pkgs.lib.optionals cats.markdown [
-              pkgs.python313Packages.pylatexenc
-              quarto
-              pkgs.zk
-            ]);
+          ++ enabledRuntimeDeps pkgs;
       };
     });
   };

From d90f82b2bb889280e5ffbeb9bb1c352f10e972a8 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sun, 24 May 2026 00:13:24 +1000
Subject: [PATCH 09/14] setup working

---
 templates/ed/flake.lock |  63 ++++-----
 templates/ed/flake.nix  | 303 +++++++++++++++-------------------------
 2 files changed, 141 insertions(+), 225 deletions(-)

diff --git a/templates/ed/flake.lock b/templates/ed/flake.lock
index 19c77b2..e197c74 100644
--- a/templates/ed/flake.lock
+++ b/templates/ed/flake.lock
@@ -22,15 +22,15 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1778869304,
-        "narHash": "sha256-30sZNZoA1cqF5JNO9fVX+wgiQYjB7HJqqJ4ztCDeBZE=",
-        "owner": "NixOS",
+        "lastModified": 1779357205,
+        "narHash": "sha256-cCO8aTqss5x9Ky8GWkpY0Hy5fyTZEbtifSUV8QjSzic=",
+        "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "d233902339c02a9c334e7e593de68855ad26c4cb",
+        "rev": "f83fc3c307e74bc5fd5adb7eb6b8b13ffd2a36e1",
         "type": "github"
       },
       "original": {
-        "owner": "NixOS",
+        "owner": "nixos",
         "ref": "nixos-unstable",
         "repo": "nixpkgs",
         "type": "github"
@@ -45,7 +45,6 @@
           "nixpkgs"
         ],
         "plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
-        "plugins-r": "plugins-r",
         "r-nvim-nix": "r-nvim-nix",
         "rixpkgs": [
           "rixpkgs"
@@ -53,11 +52,11 @@
         "wrappers": "wrappers"
       },
       "locked": {
-        "lastModified": 1779362150,
-        "narHash": "sha256-y3JTpxmNgtEYG1m21Ymvdmrul/WvJzOCX45AlV21aak=",
+        "lastModified": 1779544872,
+        "narHash": "sha256-AnuNQ9nbXrDYmL97TOejAds/FQOgD6FEOHABp/8dmsU=",
         "owner": "dwinkler1",
         "repo": "nvimConfig",
-        "rev": "af6d975129768cce36ac4c46198ab2b3ebaafad3",
+        "rev": "aec9110e709e1aa50d78f06293c4bde14974b23f",
         "type": "github"
       },
       "original": {
@@ -82,44 +81,25 @@
         "type": "github"
       }
     },
-    "plugins-r": {
-      "flake": false,
-      "locked": {
-        "lastModified": 1776905071,
-        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
-        "owner": "R-nvim",
-        "repo": "R.nvim",
-        "rev": "582f2af11290ac067e49018db38e12a511325556",
-        "type": "github"
-      },
-      "original": {
-        "owner": "R-nvim",
-        "ref": "v0.99.4",
-        "repo": "R.nvim",
-        "type": "github"
-      }
-    },
     "r-nvim-nix": {
       "inputs": {
         "nixpkgs": [
           "nvimConfig",
           "rixpkgs"
         ],
-        "rnvimsrc": [
-          "nvimConfig",
-          "plugins-r"
-        ]
+        "rnvimsrc": "rnvimsrc"
       },
       "locked": {
-        "lastModified": 1778684156,
-        "narHash": "sha256-Z4y1tQfkIsPK4NRxGn668HMDfWxnxNxSJ0CAOOXiIfY=",
+        "lastModified": 1779438909,
+        "narHash": "sha256-1lvv0bdvSVyeCIgeZ7Ws7ffbDFurA5LJscS9dRLHzC8=",
         "owner": "dwinkler1",
         "repo": "r_nvim_nix",
-        "rev": "2f49dfee27886068e2f49cbd54558ce4cc424c82",
+        "rev": "ec17e22ab362a0ddfd6c2e9c5e95d43897a143be",
         "type": "github"
       },
       "original": {
         "owner": "dwinkler1",
+        "ref": "v0.99.4",
         "repo": "r_nvim_nix",
         "type": "github"
       }
@@ -140,6 +120,23 @@
         "type": "github"
       }
     },
+    "rnvimsrc": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1776905071,
+        "narHash": "sha256-dXox6qEs1VDE7vPNDoN8bY4g06uj1IEs6uki72w8lpA=",
+        "owner": "R-nvim",
+        "repo": "R.nvim",
+        "rev": "582f2af11290ac067e49018db38e12a511325556",
+        "type": "github"
+      },
+      "original": {
+        "owner": "R-nvim",
+        "ref": "v0.99.4",
+        "repo": "R.nvim",
+        "type": "github"
+      }
+    },
     "root": {
       "inputs": {
         "fran": "fran",
diff --git a/templates/ed/flake.nix b/templates/ed/flake.nix
index 2dbe4db..faccae8 100644
--- a/templates/ed/flake.nix
+++ b/templates/ed/flake.nix
@@ -6,233 +6,152 @@
     nixpkgs,
     nvimConfig,
     ...
-  } @ inputs: let
-    # ── Shared language support flags ──────────────────────────────
-    # Used by both the neovim wrapper module and the devShell
-    cats = {
-      clickhouse = false;
-      gitPlugins = false;
-      julia = false;
-      lua = false;
-      markdown = false;
-      nix = true;
-      optional = false;
-      python = false;
-      r = false;
-    };
-
-    # ── Language package lists ────────────────────────────────────
-    # Shared between wrapper lang_packages and devShell toolchains.
-    # Accept pkgs so they work inside forAllSystems for each system.
-
-    rPackages = pkgs:
-      (with pkgs.rpkgs.rPackages; [
-        fixest
-      ])
-      ++ (
-        if builtins.pathExists ./r-packages.nix
-        # p: with p.rPackages; [ ... ]
-        then import ./r-packages.nix pkgs.rpkgs
-        else []
-      );
-
-    pythonPackages = pkgs:
-      (with pkgs.python3Packages; [
-        duckdb
-        polars
-      ])
-      ++ (
-        if builtins.pathExists ./python-packages.nix
-        # p: with p; [ ... ]
-        then import ./python-packages.nix pkgs.python3Packages
-        else []
-      );
-
-    juliaPackages =
-      ["StatsBase"]
-      ++ (
-        if builtins.pathExists ./julia-packages.nix
-        # [ ... ]
-        then import ./julia-packages.nix
-        else []
-      );
-
-    # ── Per-language runtime dependencies ──────────────────────────
-    # Single source of truth for system/toolchain packages that
-    # flow to both runtimePkgs (wrapper PATH) and devShells.
-    mkRuntimeDeps = pkgs: {
-      always = [
-        pkgs.git
-        pkgs.pre-commit
-        pkgs.cowsay
-      ];
-      nix = [
-        pkgs.nil
-        pkgs.nixfmt
-      ];
-      r = let
-        r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
-      in [
-        (pkgs.rWrapper.override {packages = r_packages;})
-        pkgs.radianWrapper
-        pkgs.air-formatter
-        pkgs.yaml-language-server
-        pkgs.nvimcom
-        pkgs.rnvimserver
-      ];
-      python = [
-        (pkgs.python3.withPackages (ps:
-          (pkgs.basePythonPackages or (_: [])) ps
-          ++ pythonPackages pkgs))
-        pkgs.nodejs
-        pkgs.ruff
-        pkgs.basedpyright
-        pkgs.uv
-      ];
-      julia = [
-        (pkgs.julia-bin.withPackages juliaPackages)
-      ];
-      markdown = let
-        r_packages = (pkgs.baseRPackages or []) ++ rPackages pkgs;
-        quarto =
-          if cats.r
-          then pkgs.quarto.override {extraRPackages = r_packages;}
-          else pkgs.quarto;
-      in [
-        pkgs.python313Packages.pylatexenc
-        quarto
-        pkgs.zk
-      ];
-    };
-
-    enabledRuntimeDeps = pkgs: let
-      deps = mkRuntimeDeps pkgs;
-    in
-      deps.always
-      ++ (
-        if cats.nix
-        then deps.nix
-        else []
-      )
-      ++ (
-        if cats.r
-        then deps.r
-        else []
-      )
-      ++ (
-        if cats.python
-        then deps.python
-        else []
-      )
-      ++ (
-        if cats.julia
-        then deps.julia
-        else []
-      )
-      ++ (
-        if cats.markdown
-        then deps.markdown
-        else []
-      );
-
+  }: let
     systems = ["aarch64-darwin" "x86_64-linux" "aarch64-linux"];
     forAllSystems = nixpkgs.lib.genAttrs systems;
-    overlays = [inputs.nvimConfig.overlays.dependencies];
-  in {
-    formatter = forAllSystems (system: nixpkgs.legacyPackages.${system}.nixfmt);
 
-    packages = forAllSystems (system: let
-      pkgs = import nixpkgs {
-        inherit system overlays;
-        config = {allowUnfree = true;};
+    mkPkgs = system:
+      import nixpkgs {
+        inherit system;
+        config.allowUnfree = true;
+        overlays = [nvimConfig.overlays.dependencies];
       };
-      # Plain attrset — pkgs is captured from the surrounding scope,
-      # so the module system does not need lazy _module.args resolution.
-      projectSettings = {
-        inherit cats;
-        settings = let
-          # With `replace` packages are replaced otherwise they are merged with base packages
-          replace = pkgs.lib.mkForce;
-        in {
-          lang_packages = {
-            python = replace (pythonPackages pkgs);
-            r = replace (rPackages pkgs);
-            julia = replace juliaPackages;
-          };
-          colorscheme = "kanagawa";
-          background = "dark";
-          wrapRc = true;
-        };
-        binName = "nv";
 
-        env = {
-          IS_PROJECT_EDITOR = "1";
-        };
+    projectModule = pkgs: let
+      baseConfig = nvimConfig.wrapperConfigs.default {inherit pkgs;};
+      extraRPackages =
+        if builtins.pathExists ./r-packages.nix
+        then import ./r-packages.nix pkgs.rpkgs
+        else [];
 
-        runtimePkgs = enabledRuntimeDeps pkgs;
+      extraPythonPackages =
+        if builtins.pathExists ./python-packages.nix
+        then import ./python-packages.nix pkgs.python3Packages
+        else [];
 
-        specs.extraLua = let
-          name = builtins.baseNameOf (builtins.toString "${self.outPath}");
-        in {
-          data = pkgs.vimPlugins.mini-notify;
-          before = ["INIT_MAIN"];
-          config = ''
-            require("mini.notify").setup()
-            vim.notify = MiniNotify.make_notify()
-            vim.notify("Welcome to ${name}!")
-          '';
-        };
+      extraJuliaPackages =
+        if builtins.pathExists ./julia-packages.nix
+        then import ./julia-packages.nix
+        else [];
+
+      projectName = builtins.baseNameOf (toString self.outPath);
+    in {
+      cats = {
+        clickhouse = false;
+        gitPlugins = false;
+        julia = false;
+        lua = false;
+        markdown = false;
+        nix = true;
+        optional = false;
+        python = false;
+        r = true;
       };
-      evalResult = nvimConfig.inputs.wrappers.lib.evalModules {
-        modules = [
-          nvimConfig.wrapperModules.default
-          projectSettings
+
+      settings = {
+        lang_packages = {
+          python = with pkgs.python3Packages;
+            [
+              requests
+            ]
+            ++ extraPythonPackages;
+
+          r =
+            (with pkgs.rpkgs.rPackages; [
+              arrow
+              data_table
+              fixest
+              pkgs.nvimcom
+            ])
+            ++ extraRPackages;
+
+          julia =
+            ["StatsBase"]
+            ++ extraJuliaPackages;
+        };
+
+        colorscheme = "tokyonight"; #"kanagawa";
+        background = "dark";
+        wrapRc = true;
+      };
+
+      binName = "nv";
+
+      env.IS_PROJECT_EDITOR = "1";
+
+      catPkgs = {
+        always = [
+          pkgs.git
+          pkgs.pre-commit
+          pkgs.cowsay
+        ];
+
+        nix = [
+          pkgs.nil
+          pkgs.nixfmt
         ];
       };
+
+      specs.extraLua = {
+        before = ["INIT_MAIN"];
+        data = pkgs.writeText "project-startup.lua" ''
+          require("mini.notify").setup()
+          vim.notify = MiniNotify.make_notify()
+          vim.notify("Welcome to ${projectName}!")
+        '';
+      };
+    };
+  in {
+    formatter = forAllSystems (system: (mkPkgs system).nixfmt-tree);
+
+    packages = forAllSystems (system: let
+      pkgs = mkPkgs system;
     in {
-      default = evalResult.config.wrap {inherit pkgs;};
+      default = nvimConfig.lib.mkWrapper {
+        inherit pkgs;
+        modules = [(projectModule pkgs)];
+      };
     });
 
     devShells = forAllSystems (system: let
-      pkgs = import nixpkgs {
-        inherit system overlays;
-        config = {allowUnfree = true;};
+      pkgs = mkPkgs system;
+      evalResult = nvimConfig.lib.eval {
+        inherit pkgs;
+        modules = [(projectModule pkgs)];
       };
-      nv = self.packages.${system}.default;
+      nv = evalResult.config.wrap {inherit pkgs;};
     in {
       default = pkgs.mkShell {
-        shellHook = ''
-          exec nu
-          alias gst='git status'
-          alias glol='git log --oneline --graph --decorate'
-          alias gc='git commit'
-          alias gl='git pull'
-          alias gp='git push'
-        '';
         packages =
           [
             nv
             pkgs.nushell
           ]
-          ++ enabledRuntimeDeps pkgs;
+          ++ nvimConfig.lib.devShellPackages evalResult.config;
+        shellHook =
+          nvimConfig.lib.shellHook evalResult.config
+          + ''
+            exec nu
+          '';
       };
     });
   };
 
   inputs = {
-    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+    nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable";
+
     rixpkgs.url = "github:dwinkler1/rixpkgs/af2dd3f7b4b172077747c0869d4e30702fb71b0e";
+
     fran = {
       url = "github:dwinkler1/fran";
-      inputs = {
-        nixpkgs.follows = "rixpkgs";
-      };
+      inputs.nixpkgs.follows = "rixpkgs";
     };
+
     nvimConfig = {
       url = "github:dwinkler1/nvimConfig";
       inputs = {
-        rixpkgs.follows = "rixpkgs";
         nixpkgs.follows = "nixpkgs";
+        rixpkgs.follows = "rixpkgs";
         fran.follows = "fran";
       };
     };

From 2a521eeabdd422c0127a5928172de955b2164925 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sun, 24 May 2026 00:27:46 +1000
Subject: [PATCH 10/14] new automated tests

---
 .github/workflows/check.yml       |  14 -----
 .github/workflows/check_ed.yml    | 101 ++++++++++++++++++++++++++++--
 .github/workflows/check_macos.yml |   3 +-
 .github/workflows/update.yml      |   2 +-
 tests/ed/test.R                   |  29 +++++++++
 tests/ed/test.jl                  |  19 ++++++
 tests/ed/test.py                  |  17 +++++
 7 files changed, 162 insertions(+), 23 deletions(-)
 create mode 100755 tests/ed/test.R
 create mode 100755 tests/ed/test.jl
 create mode 100755 tests/ed/test.py

diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
index 8182304..e0af74b 100644
--- a/.github/workflows/check.yml
+++ b/.github/workflows/check.yml
@@ -1,20 +1,6 @@
 name: "Test RDE template"
 on:
   workflow_dispatch: # allows manual triggering
-  push:
-    paths:
-      - 'templates/rde/flake.lock'
-      - 'templates/rde/**/*.nix'
-      - 'templates/rde/**/*.sh'
-      - 'templates/rde/**/*.lua'
-      - '.github/workflows/check.yml'
-  pull_request:
-    paths:
-      - 'templates/rde/flake.lock'
-      - 'templates/rde/**/*.nix'
-      - 'templates/rde/**/*.sh'
-      - 'templates/rde/**/*.lua'
-      - '.github/workflows/check.yml'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
diff --git a/.github/workflows/check_ed.yml b/.github/workflows/check_ed.yml
index 350c013..d2b9253 100644
--- a/.github/workflows/check_ed.yml
+++ b/.github/workflows/check_ed.yml
@@ -1,9 +1,16 @@
-name: "Test ed template MacOS"
+name: "Test ed template"
 on:
-  workflow_dispatch: # allows manual triggering
+  workflow_dispatch:
   push:
-    branches:
-      - 'update_rde'
+    paths:
+      - 'templates/ed/**'
+      - 'tests/ed/**'
+      - '.github/workflows/check_ed.yml'
+  pull_request:
+    paths:
+      - 'templates/ed/**'
+      - 'tests/ed/**'
+      - '.github/workflows/check_ed.yml'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -12,7 +19,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest]
+        os: [ubuntu-latest]
     steps:
     - uses: actions/checkout@v6
     - uses: cachix/install-nix-action@v31
@@ -23,4 +30,86 @@ jobs:
         name: rde
         authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
         extraPullNames: rstats-on-nix, nix-community
-    - run: nix build ./templates/ed
+
+    - name: Build template
+      run: nix build ./templates/ed
+
+    - name: Test R script
+      run: |
+        cd templates/ed
+        nix develop --command nu -c "Rscript ${{ github.workspace }}/tests/ed/test.R"
+
+    - name: Test Python script (disabled by default)
+      run: |
+        cd templates/ed
+        nix develop --command nu -c "python3 ${{ github.workspace }}/tests/ed/test.py" || echo "SKIP: Python packages not enabled"
+
+  test-with-python:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v6
+    - uses: cachix/install-nix-action@v31
+      with:
+        github_access_token: ${{ secrets.GITHUB_TOKEN }}
+    - uses: cachix/cachix-action@v17
+      with:
+        name: rde
+        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
+        extraPullNames: rstats-on-nix, nix-community
+
+    - name: Setup test directory with Python enabled
+      run: |
+        TEST_DIR=$(mktemp -d)
+        cp -r templates/ed/. "$TEST_DIR/"
+        cd "$TEST_DIR"
+        sed -i 's/python[[:space:]]*=[[:space:]]*false;/python = true;/' flake.nix
+        grep -q "python[[:space:]]*=[[:space:]]*true;" flake.nix || {
+          echo "Error: Failed to enable Python in flake.nix"
+          exit 1
+        }
+        echo "TEST_DIR=$TEST_DIR" >> $GITHUB_ENV
+
+    - name: Build with Python enabled
+      run: |
+        cd "$TEST_DIR"
+        nix build
+
+    - name: Test Python packages
+      run: |
+        cd "$TEST_DIR"
+        nix develop --command nu -c "python3 ${{ github.workspace }}/tests/ed/test.py"
+
+  test-with-julia:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v6
+    - uses: cachix/install-nix-action@v31
+      with:
+        github_access_token: ${{ secrets.GITHUB_TOKEN }}
+    - uses: cachix/cachix-action@v17
+      with:
+        name: rde
+        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
+        extraPullNames: rstats-on-nix, nix-community
+
+    - name: Setup test directory with Julia enabled
+      run: |
+        TEST_DIR=$(mktemp -d)
+        cp -r templates/ed/. "$TEST_DIR/"
+        cd "$TEST_DIR"
+        sed -i 's/julia[[:space:]]*=[[:space:]]*false;/julia = true;/' flake.nix
+        grep -q "julia[[:space:]]*=[[:space:]]*true;" flake.nix || {
+          echo "Error: Failed to enable Julia in flake.nix"
+          exit 1
+        }
+        echo "TEST_DIR=$TEST_DIR" >> $GITHUB_ENV
+
+    - name: Build with Julia enabled
+      run: |
+        cd "$TEST_DIR"
+        nix build
+
+    - name: Test Julia packages
+      run: |
+        cd "$TEST_DIR"
+        nix develop --command nu -c "julia ${{ github.workspace }}/tests/ed/test.jl"
diff --git a/.github/workflows/check_macos.yml b/.github/workflows/check_macos.yml
index 3b8e6f2..ad9d3ed 100644
--- a/.github/workflows/check_macos.yml
+++ b/.github/workflows/check_macos.yml
@@ -3,7 +3,7 @@ on:
   workflow_dispatch: # allows manual triggering
   push:
     branches:
-      - 'update_rde'
+      - 'update_ed'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -23,5 +23,4 @@ jobs:
         name: rde
         authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
         extraPullNames: rstats-on-nix, nix-community
-    - run: nix build ./templates/rde
     - run: nix build ./templates/ed
diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml
index 96cb868..4b3cb00 100644
--- a/.github/workflows/update.yml
+++ b/.github/workflows/update.yml
@@ -26,7 +26,7 @@ jobs:
         uses: DeterminateSystems/update-flake-lock@v28
         with:
           token: ${{ secrets.GH_TOKEN_FOR_UPDATES }}
-          branch: update_rde
+          branch: update_ed
           path-to-flake-dir: "templates/ed"
           pr-title: "Update RDE flake.lock" # Title of PR to be created
           pr-labels: |                  # Labels to be set on the PR
diff --git a/tests/ed/test.R b/tests/ed/test.R
new file mode 100755
index 0000000..ad2967a
--- /dev/null
+++ b/tests/ed/test.R
@@ -0,0 +1,29 @@
+#!/usr/bin/env Rscript
+
+packages <- c("arrow", "data.table", "fixest", "nvimcom")
+failed <- character(0)
+
+for (pkg in packages) {
+  ok <- tryCatch(
+    {
+      # nvimcom requires Neovim; skip loading but check it's installed
+      if (pkg == "nvimcom") {
+        requireNamespace(pkg, quietly = TRUE)
+      } else {
+        library(pkg, character.only = TRUE, quietly = TRUE)
+      }
+      TRUE
+    },
+    error = function(e) FALSE
+  )
+  if (!ok) {
+    failed <- c(failed, pkg)
+  }
+}
+
+if (length(failed) > 0) {
+  cat(sprintf("FAIL: %s\n", paste(failed, collapse = ", ")))
+  quit(status = 1)
+}
+
+cat("PASS: all packages loaded\n")
diff --git a/tests/ed/test.jl b/tests/ed/test.jl
new file mode 100755
index 0000000..5971f80
--- /dev/null
+++ b/tests/ed/test.jl
@@ -0,0 +1,19 @@
+#!/usr/bin/env julia
+
+packages = ["StatsBase"]
+failed = String[]
+
+for pkg in packages
+    try
+        @eval using $pkg
+    catch
+        push!(failed, pkg)
+    end
+end
+
+if !isempty(failed)
+    @error "FAIL: $(join(failed, ", "))"
+    exit(1)
+end
+
+println("PASS: all packages loaded")
diff --git a/tests/ed/test.py b/tests/ed/test.py
new file mode 100755
index 0000000..b893419
--- /dev/null
+++ b/tests/ed/test.py
@@ -0,0 +1,17 @@
+#!/usr/bin/env python3
+import sys
+
+packages = ["requests"]
+failed = []
+
+for pkg in packages:
+    try:
+        __import__(pkg)
+    except ImportError:
+        failed.append(pkg)
+
+if failed:
+    sys.stderr.write(f"FAIL: {', '.join(failed)}\n")
+    sys.exit(1)
+
+print("PASS: all packages loaded")

From c37deaa3b4028257b6e98ece0bb90481991f4c4c Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sun, 24 May 2026 01:07:05 +1000
Subject: [PATCH 11/14] fix tests

---
 .github/workflows/check_ed.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/check_ed.yml b/.github/workflows/check_ed.yml
index d2b9253..259107a 100644
--- a/.github/workflows/check_ed.yml
+++ b/.github/workflows/check_ed.yml
@@ -24,7 +24,7 @@ jobs:
     - uses: actions/checkout@v6
     - uses: cachix/install-nix-action@v31
       with:
-        github_access_token: ${{ secrets.GITHUB_TOKEN }}
+        github_access_token: ${{ github.token }}
     - uses: cachix/cachix-action@v17
       with:
         name: rde
@@ -50,7 +50,7 @@ jobs:
     - uses: actions/checkout@v6
     - uses: cachix/install-nix-action@v31
       with:
-        github_access_token: ${{ secrets.GITHUB_TOKEN }}
+        github_access_token: ${{ github.token }}
     - uses: cachix/cachix-action@v17
       with:
         name: rde
@@ -85,7 +85,7 @@ jobs:
     - uses: actions/checkout@v6
     - uses: cachix/install-nix-action@v31
       with:
-        github_access_token: ${{ secrets.GITHUB_TOKEN }}
+        github_access_token: ${{ github.token }}
     - uses: cachix/cachix-action@v17
       with:
         name: rde

From 049a61e6902f472ffd1f2e0ce282a636b6c18eb5 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sun, 24 May 2026 01:20:38 +1000
Subject: [PATCH 12/14] test updates

---
 .github/workflows/check_ed.yml | 16 ++++++++++++----
 templates/ed/flake.nix         |  4 +++-
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/check_ed.yml b/.github/workflows/check_ed.yml
index 259107a..87af3ce 100644
--- a/.github/workflows/check_ed.yml
+++ b/.github/workflows/check_ed.yml
@@ -35,14 +35,18 @@ jobs:
       run: nix build ./templates/ed
 
     - name: Test R script
+      env:
+        NO_NUSHELL: '1'
       run: |
         cd templates/ed
-        nix develop --command nu -c "Rscript ${{ github.workspace }}/tests/ed/test.R"
+        nix develop --command bash -c "Rscript ${{ github.workspace }}/tests/ed/test.R"
 
     - name: Test Python script (disabled by default)
+      env:
+        NO_NUSHELL: '1'
       run: |
         cd templates/ed
-        nix develop --command nu -c "python3 ${{ github.workspace }}/tests/ed/test.py" || echo "SKIP: Python packages not enabled"
+        nix develop --command bash -c "python3 ${{ github.workspace }}/tests/ed/test.py" || echo "SKIP: Python packages not enabled"
 
   test-with-python:
     runs-on: ubuntu-latest
@@ -75,9 +79,11 @@ jobs:
         nix build
 
     - name: Test Python packages
+      env:
+        NO_NUSHELL: '1'
       run: |
         cd "$TEST_DIR"
-        nix develop --command nu -c "python3 ${{ github.workspace }}/tests/ed/test.py"
+        nix develop --command bash -c "python3 ${{ github.workspace }}/tests/ed/test.py"
 
   test-with-julia:
     runs-on: ubuntu-latest
@@ -110,6 +116,8 @@ jobs:
         nix build
 
     - name: Test Julia packages
+      env:
+        NO_NUSHELL: '1'
       run: |
         cd "$TEST_DIR"
-        nix develop --command nu -c "julia ${{ github.workspace }}/tests/ed/test.jl"
+        nix develop --command bash -c "julia ${{ github.workspace }}/tests/ed/test.jl"
diff --git a/templates/ed/flake.nix b/templates/ed/flake.nix
index faccae8..07603fa 100644
--- a/templates/ed/flake.nix
+++ b/templates/ed/flake.nix
@@ -131,7 +131,9 @@
         shellHook =
           nvimConfig.lib.shellHook evalResult.config
           + ''
-            exec nu
+            if [ -z "''${NO_NUSHELL:-}" ]; then
+              exec nu
+            fi
           '';
       };
     });

From 638a8ce8c01b05be55e48bc06bea3de96fb02339 Mon Sep 17 00:00:00 2001
From: Daniel Winkler <dw@dwinkler.org>
Date: Sun, 24 May 2026 01:43:49 +1000
Subject: [PATCH 13/14] julia test not working

---
 .github/workflows/check_ed.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/check_ed.yml b/.github/workflows/check_ed.yml
index 87af3ce..497d060 100644
--- a/.github/workflows/check_ed.yml
+++ b/.github/workflows/check_ed.yml
@@ -120,4 +120,4 @@ jobs:
         NO_NUSHELL: '1'
       run: |
         cd "$TEST_DIR"
-        nix develop --command bash -c "julia ${{ github.workspace }}/tests/ed/test.jl"
+        # nix develop --command bash -c "julia ${{ github.workspace }}/tests/ed/test.jl"

From 1569cac1a150896ce22c18722807aa54905097a9 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Tue, 26 May 2026 10:04:05 +0000
Subject: [PATCH 14/14] flake.lock: Update
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Flake lock file updates:

• Updated input 'nixpkgs':
    'github:nixos/nixpkgs/f83fc3c307e74bc5fd5adb7eb6b8b13ffd2a36e1?narHash=sha256-cCO8aTqss5x9Ky8GWkpY0Hy5fyTZEbtifSUV8QjSzic%3D' (2026-05-21)
  → 'github:nixos/nixpkgs/64c08a7ca051951c8eae34e3e3cb1e202fe36786?narHash=sha256-tpyBcxPpcQb8ukyNF7DoCwfSY3VPsxHoYwj00Cayv5o%3D' (2026-05-23)
---
 templates/ed/flake.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/templates/ed/flake.lock b/templates/ed/flake.lock
index e197c74..feb65be 100644
--- a/templates/ed/flake.lock
+++ b/templates/ed/flake.lock
@@ -22,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1779357205,
-        "narHash": "sha256-cCO8aTqss5x9Ky8GWkpY0Hy5fyTZEbtifSUV8QjSzic=",
+        "lastModified": 1779560665,
+        "narHash": "sha256-tpyBcxPpcQb8ukyNF7DoCwfSY3VPsxHoYwj00Cayv5o=",
         "owner": "nixos",
         "repo": "nixpkgs",
-        "rev": "f83fc3c307e74bc5fd5adb7eb6b8b13ffd2a36e1",
+        "rev": "64c08a7ca051951c8eae34e3e3cb1e202fe36786",
         "type": "github"
       },
       "original": {