Fix stdin deadlock and exit code rewrite logic

run.go

@@ -174,10 +174,8 @@ func runFile(file ShoutFile, opts RunOptions) FileResult {
 		}
 	}
 
-	_, _ = io.WriteString(stdin, script)
-	stdin.Close()
-
-	// Read stdout with timeout
+	// Read stdout with timeout — must start reader BEFORE writing to stdin
+	// to avoid deadlock when pipe buffers fill in both directions.
 	totalTimeout := opts.Timeout * time.Duration(len(file.Commands))
 	type readResult struct {
 		data []byte
@@ -189,6 +187,9 @@ func runFile(file ShoutFile, opts RunOptions) FileResult {
 		ch <- readResult{data, err}
 	}()
 
+	_, _ = io.WriteString(stdin, script)
+	stdin.Close()
+
 	var output []byte
 	select {
 	case r := <-ch:

update.go

@@ -53,16 +53,45 @@ func rewriteFile(file ShoutFile, results []CommandResult, originalContent string
 				}
 			}
 
-			// If wildcards match, keep original
-			if matchOutput(cmd.Expected, result.Actual) {
+			outputMatch := matchOutput(cmd.Expected, result.Actual)
+			ecMatch := exitCodeOK(cmd.ExitCodeType, cmd.ExitCodeValue, result.ExitCode)
+
+			if outputMatch && ecMatch {
+				// Both match — preserve original verbatim
 				output = append(output, oldExpectedRaw...)
+			} else if outputMatch {
+				// Output matches but exit code changed — preserve output, fix exit code
+				raw := oldExpectedRaw
+				rawTrailing := 0
+				for k := len(raw) - 1; k >= 0; k-- {
+					if raw[k] == "" {
+						rawTrailing++
 					} else {
+						break
+					}
+				}
+				content := raw[:len(raw)-rawTrailing]
+				// Strip old exit code marker if present
+				if len(content) > 0 && exitCodeMarkerRe.MatchString(content[len(content)-1]) {
+					content = content[:len(content)-1]
+				}
+				output = append(output, content...)
+				marker := updateExitCodeMarker(cmd, result.ExitCode)
+				if marker != "" {
+					output = append(output, marker)
+				} else if len(content) > 0 && exitCodeMarkerRe.MatchString(content[len(content)-1]) {
+					output = append(output, "[0]")
+				}
+				for k := 0; k < rawTrailing; k++ {
+					output = append(output, "")
+				}
+			} else {
+				// Output doesn't match — rewrite everything
 				output = append(output, result.Actual...)
-				if result.ExitCode != 0 {
-					output = append(output, fmt.Sprintf("[%d]", result.ExitCode))
+				marker := updateExitCodeMarker(cmd, result.ExitCode)
+				if marker != "" {
+					output = append(output, marker)
 				} else if len(result.Actual) > 0 && exitCodeMarkerRe.MatchString(result.Actual[len(result.Actual)-1]) {
-					// Actual output's last line looks like an exit code marker.
-					// Add an explicit [0] to prevent parser from consuming it.
 					output = append(output, "[0]")
 				}
 				for k := 0; k < trailingBlanks; k++ {
@@ -79,3 +108,15 @@ func rewriteFile(file ShoutFile, results []CommandResult, originalContent string
 
 	return strings.Join(output, "\n")
 }
+
+// updateExitCodeMarker returns the exit code marker to write, preserving [*]
+// wildcards when the command still exits non-zero.
+func updateExitCodeMarker(cmd Command, actualExitCode int) string {
+	if cmd.ExitCodeType == ExitCodeWildcard && actualExitCode != 0 {
+		return "[*]"
+	}
+	if actualExitCode != 0 {
+		return fmt.Sprintf("[%d]", actualExitCode)
+	}
+	return ""
+}