CLI: a closed stdout pipe exits 141 silently (was E_INTERNAL); example avoids head under pipefail

Found by the P10 fresh-VM run: `simurg inspect … | head` raised BrokenPipeError, reported as
an internal error, and stopped examples/gsa_demo.sh (set -o pipefail). run_guarded now flushes
stdout inside the guard and maps BrokenPipeError to ExitCode.SIGPIPE (141) without a message.
p10.sh: SKIP_DOCKER/SKIP_CONDA, clearer digest report; p10t.sh runs build+pip+tutorial only.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

examples/gsa_demo.sh

@@ -30,7 +30,7 @@ mkdir -p "$OUT"
 # Optional subset: symlink the first N IDAT pairs into $OUT/idats (same <barcode>/<barcode>_<pos>_<ch>.idat layout).
 if [[ $N -gt 0 ]]; then
   rm -rf "$OUT/idats"
-  find "$IDATS" -name '*_Grn.idat' | sort | head -n "$N" | while read -r g; do
+  find "$IDATS" -name '*_Grn.idat' | sort | sed -n "1,${N}p" | while read -r g; do
     b=$(basename "$(dirname "$g")"); mkdir -p "$OUT/idats/$b"
     ln -s "$(realpath "$g")" "$OUT/idats/$b/"; ln -s "$(realpath "${g%_Grn.idat}_Red.idat")" "$OUT/idats/$b/"
   done
@@ -38,12 +38,12 @@ if [[ $N -gt 0 ]]; then
 fi
 
 echo "== 1. inspect the inputs"
-$SIMURG inspect "$BPM" "$EGT" | head -20
+$SIMURG inspect "$BPM" "$EGT" | sed -n 1,20p   # sed reads to the end: no SIGPIPE under pipefail
 
 echo "== 2. genotype: GTC v5 per sample, sample_summary.tsv, control-probe QC, contamination, relatedness"
 $SIMURG genotype --bpm "$BPM" --egt "$EGT" --csv "$CSV" --idats "$IDATS" --out "$OUT/gtc" \
   --qc-profile genotyping --threads "$THREADS" --force
-column -t -s$'\t' "$OUT/gtc/sample_summary.tsv" | cut -c1-150 | head -8
+column -t -s$'\t' "$OUT/gtc/sample_summary.tsv" | cut -c1-150 | sed -n 1,8p
 
 echo "== 3. HTML QC report + QC table"
 $SIMURG qc report --data "$OUT/gtc" --out "$OUT/qc_report" --output-format both