update project design

run_all.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+# Run the current learning project workflow end to end.
+#
+# This is intentionally simpler than a targets pipeline.
+# It gives us one command that runs the simulation smoke check and renders the
+# Quarto notebooks while the project is still small.
+
+set -euo pipefail
+
+# Make the script work even if it is called from another directory.
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+cd "$script_dir"
+
+mkdir -p "outputs/reports"
+
+Rscript "scripts/01_simulate_icu_data.R"
+
+quarto render "notebooks/01_target_trial_basics.qmd" --output-dir "../outputs/reports"
+quarto render "notebooks/02_explore_simulated_data.qmd" --output-dir "../outputs/reports"
+
+printf '\nWorkflow complete. Reports are in outputs/reports/.\n'