Refactor template: extract scripts, overlays, and hosts into separate modules

Co-authored-by: dwinkler1 <22460147+dwinkler1@users.noreply.github.com>

templates/rde/scripts/updateDeps.sh

@@ -0,0 +1,29 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+echo "🔄 Updating project dependencies..."
+
+RVER=$( wget -qO- 'https://raw.githubusercontent.com/ropensci/rix/refs/heads/main/inst/extdata/available_df.csv' | tail -n 1 | head -n 1 | cut -d',' -f4 | tr -d '"' ) &&\
+
+sed -i  "s|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}\";|rixpkgs.url = \"github:rstats-on-nix/nixpkgs/$RVER\";|" flake.nix
+echo "✅ R date is $RVER"
+
+nix flake update
+echo "✅ Flake inputs updated"
+
+if [[ -f "pyproject.toml" ]]; then
+  uv sync --upgrade
+  echo "✅ Python dependencies updated"
+fi
+
+if [[ -f "Project.toml" ]]; then
+  @defaultPackageName@-jl -e "using Pkg; Pkg.update()"
+  echo "✅ Julia dependencies updated"
+fi
+
+if [[ -f "devenv.nix" ]]; then
+  devenv update
+  echo "✅ Devenv dependencies updated"
+fi
+
+echo "🎉 All dependencies updated!"