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] 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
     ]