fix: prompt.md via stdin now combines with codex flags

Options like -s read-only routed execution into the /dev/null branch,
so codex got no prompt at all. codex natively appends piped stdin as
a <stdin> block, so feeding prompt.md unconditionally is safe.

tests/test-run.sh

@@ -9,7 +9,7 @@ trap 'rm -rf "$TMP"' EXIT
 CODEX_BIN=$HERE/stub-ok/codex "$RUN" "$TMP/ok" exec "hello"
 [[ $(cat "$TMP/ok/status") == ok ]]
 [[ $(cat "$TMP/ok/thread_id") == test-thread-123 ]]
-[[ $(cat "$TMP/ok/last.md") == "stub answer" ]]
+[[ $(cat "$TMP/ok/last.md") == "stub answer|" ]]
 
 # 2. stall -> watchdog kills, status stalled, exit nonzero
 if CODEX_BIN=$HERE/stub-hang/codex CODEX_STALL_TIMEOUT=4 CODEX_WATCH_INTERVAL=2 \
@@ -23,5 +23,12 @@ fi
 mkdir -p "$TMP/stdin"; echo "prompt from file" > "$TMP/stdin/prompt.md"
 CODEX_BIN=$HERE/stub-ok/codex "$RUN" "$TMP/stdin" exec
 [[ $(cat "$TMP/stdin/status") == ok ]]
+[[ $(cat "$TMP/stdin/last.md") == "stub answer|prompt from file" ]]
+
+# 4. prompt.md + codex flags -> stdin still delivered (regression: options ate the prompt)
+mkdir -p "$TMP/flags"; echo "prompt with flags" > "$TMP/flags/prompt.md"
+CODEX_BIN=$HERE/stub-ok/codex "$RUN" "$TMP/flags" exec -s read-only
+[[ $(cat "$TMP/flags/status") == ok ]]
+[[ $(cat "$TMP/flags/last.md") == "stub answer|prompt with flags" ]]
 
 echo "ALL PASS"