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

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

templates/rde/scripts/initProject.sh

@@ -0,0 +1,104 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+PROJECT_NAME="${1:-@defaultPackageName@}"
+
+echo "🚀 Setting up project: $PROJECT_NAME"
+
+# Create directory structure
+directories=(
+  "data/raw"
+  "data/processed"
+  "data/interim"
+  "docs"
+  "figures"
+  "tables"
+  "src/analysis"
+  "src/data_prep"
+  "src/explore"
+  "src/utils"
+)
+
+for dir in "${directories[@]}"; do
+  if [[ ! -d "$dir" ]]; then
+    mkdir -p "$dir"
+    echo "✓ Created $dir/"
+  fi
+done
+
+# Create essential files
+if [[ ! -f "README.md" ]]; then
+  cat > README.md << 'EOF'
+# RDE
+
+## Project Structure
+- `data/`: Data files (gitignored)
+- `docs/`: Documentation
+- `figures/`: Output figures
+- `tables/`: Output tables
+- `src/`: Source code
+
+EOF
+fi
+
+# Initialize git
+if [[ ! -d ".git" ]]; then
+  git init
+  echo "✓ Initialized Git repository and added: flake.nix, flake.lock"
+fi
+# Check if files are already staged/tracked before adding
+if ! git diff --cached --name-only | grep -q "flake.nix\|flake.lock" &&
+   ! git ls-files --error-unmatch flake.nix flake.lock >/dev/null 2>&1; then
+  echo "✓ Adding flake.nix, flake.lock to Git repository"
+  git add flake.nix flake.lock
+else
+  echo "✓ flake.nix, flake.lock already tracked/staged in Git"
+fi
+# Create .gitignore
+if [[ ! -f ".gitignore" ]]; then
+  cat > .gitignore << 'EOF'
+# Data files
+data/
+*.csv
+*.docx
+*.xlsx
+*.parquet
+
+# R specific
+.Rproj.user/
+.Rhistory
+.RData
+.Ruserdata
+*.Rproj
+.Rlibs/
+
+# Python specific
+__pycache__/
+*.pyc
+.pytest_cache/
+.venv/
+
+# Jupyter
+.ipynb_checkpoints/
+
+# IDE
+.vscode/
+.idea/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Devenv
+.devenv*
+devenv.local.nix
+
+# direnv
+.direnv
+
+# pre-commit
+.pre-commit-config.yaml
+EOF
+fi
+
+echo "✅ Project setup completed successfully!"