From cc69aa34f84d35faabf26ba148d4dbf71e1595f3 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 11 Jan 2026 19:32:05 +0000
Subject: [PATCH] Add clarifying comments based on code review feedback

Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>
---
 templates/rde/lib/shell-hook.nix    | 1 +
 templates/rde/overlays/r.nix        | 2 ++
 templates/rde/scripts/updateDeps.sh | 3 +++
 3 files changed, 6 insertions(+)

diff --git a/templates/rde/lib/shell-hook.nix b/templates/rde/lib/shell-hook.nix
index 3a4a9d6..56b2159 100644
--- a/templates/rde/lib/shell-hook.nix
+++ b/templates/rde/lib/shell-hook.nix
@@ -31,6 +31,7 @@ in ''
   echo "${shellCmds}"
   echo "=========================================================================="
   echo ""
+  # Auto-activate devenv shell if devenv.nix exists (can be disabled in config)
   ${pkgs.lib.optionalString enabledPackages.devenv "${defaultPackageName}-activateDevenv"}
   echo ""
 ''
diff --git a/templates/rde/overlays/r.nix b/templates/rde/overlays/r.nix
index 4b3136d..b40bee9 100644
--- a/templates/rde/overlays/r.nix
+++ b/templates/rde/overlays/r.nix
@@ -13,6 +13,8 @@ final: prev: let
     ++ (with final.extraRPackages; [
       httpgd
     ])
+    # Import custom R packages from project root if file exists
+    # Users can create r-packages.nix in their project to add more packages
     ++ (prev.lib.optional (builtins.pathExists ./r-packages.nix) (import ./r-packages.nix final.rpkgs));
 in {
   quarto = final.rpkgs.quarto.override {extraRPackages = reqPkgs;};
diff --git a/templates/rde/scripts/updateDeps.sh b/templates/rde/scripts/updateDeps.sh
index d0d0c9c..61310a4 100644
--- a/templates/rde/scripts/updateDeps.sh
+++ b/templates/rde/scripts/updateDeps.sh
@@ -3,8 +3,11 @@ set -euo pipefail
 
 echo "🔄 Updating project dependencies..."
 
+# Fetch latest R version from rstats-on-nix
+# This command chain: downloads CSV, extracts last line, gets 4th field (date), removes quotes
 RVER=$( wget -qO- 'https://raw.githubusercontent.com/ropensci/rix/refs/heads/main/inst/extdata/available_df.csv' | tail -n 1 | head -n 1 | cut -d',' -f4 | tr -d '"' ) &&\
 
+# Update rixpkgs date in flake.nix
 sed -i  "s|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}\";|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/$RVER\";|" flake.nix
 echo "✅ R date is $RVER"