diff --git a/parse.go b/parse.go
index 623211b..639b89b 100644
--- a/parse.go
+++ b/parse.go
@@ -12,6 +12,8 @@ func stripComment(line string) string {
 	for i := 0; i < len(line); i++ {
 		ch := line[i]
 		switch {
+		case ch == '\\' && !inSingle:
+			i++ // skip escaped character (backslash escapes in double-quoted and unquoted contexts)
 		case ch == '\'' && !inDouble:
 			inSingle = !inSingle
 		case ch == '"' && !inSingle:
diff --git a/run.go b/run.go
index 887c61c..34307a8 100644
--- a/run.go
+++ b/run.go
@@ -1,6 +1,8 @@
 package main
 
 import (
+	"crypto/rand"
+	"fmt"
 	"io"
 	"os"
 	"os/exec"
@@ -11,7 +13,11 @@ import (
 	"time"
 )
 
-const sentinelPrefix = "__SHOUT_SENTINEL_"
+func newSentinelPrefix() string {
+	b := make([]byte, 8)
+	_, _ = rand.Read(b)
+	return fmt.Sprintf("__SHOUT_%x_", b)
+}
 
 type RunOptions struct {
 	CleanEnv  bool
@@ -22,7 +28,7 @@ type RunOptions struct {
 	OnCommand func(Command)
 }
 
-func buildScript(commands []Command) string {
+func buildScript(commands []Command, sentinelPrefix string) string {
 	var b strings.Builder
 	b.WriteString("exec 2>&1\n")
 	for i, cmd := range commands {
@@ -33,7 +39,7 @@ func buildScript(commands []Command) string {
 	return b.String()
 }
 
-func parseSentinelOutput(raw string, commandCount int) (outputs [][]string, exitCodes []int) {
+func parseSentinelOutput(raw string, commandCount int, sentinelPrefix string) (outputs [][]string, exitCodes []int) {
 	re := regexp.MustCompile(regexp.QuoteMeta(sentinelPrefix) + `(\d+)_(\d+)__`)
 
 	remaining := raw
@@ -91,7 +97,8 @@ func runFile(file ShoutFile, opts RunOptions) FileResult {
 		return FileResult{File: file, TmpDir: tmpDir}
 	}
 
-	script := buildScript(file.Commands)
+	sentinel := newSentinelPrefix()
+	script := buildScript(file.Commands, sentinel)
 
 	// Build environment
 	var envMap map[string]string
@@ -115,7 +122,12 @@ func runFile(file ShoutFile, opts RunOptions) FileResult {
 
 	if len(opts.PathDirs) > 0 {
 		existing := envMap["PATH"]
-		envMap["PATH"] = strings.Join(opts.PathDirs, ":") + ":" + existing
+		prepend := strings.Join(opts.PathDirs, ":")
+		if existing != "" {
+			envMap["PATH"] = prepend + ":" + existing
+		} else {
+			envMap["PATH"] = prepend
+		}
 	}
 
 	envSlice := make([]string, 0, len(envMap))
@@ -172,12 +184,17 @@ func runFile(file ShoutFile, opts RunOptions) FileResult {
 		}
 		output = r.data
 	case <-time.After(totalTimeout):
+		if cmd.Process != nil {
+			_ = syscall.Kill(-cmd.Process.Pid, syscall.SIGKILL)
+		}
+		<-ch // drain the reader goroutine so pipe FDs are released
+		_ = cmd.Wait()
 		return FileResult{File: file, TmpDir: tmpDir, Error: "Timeout reading output"}
 	}
 
 	_ = cmd.Wait()
 
-	outputs, exitCodesList := parseSentinelOutput(string(output), len(file.Commands))
+	outputs, exitCodesList := parseSentinelOutput(string(output), len(file.Commands), sentinel)
 
 	results := make([]CommandResult, len(file.Commands))
 	for i, c := range file.Commands {
diff --git a/shout b/shout
index 440a587..7f5643b 100755
Binary files a/shout and b/shout differ
diff --git a/update.go b/update.go
index aa812b0..37fe93b 100644
--- a/update.go
+++ b/update.go
@@ -1,6 +1,7 @@
 package main
 
 import (
+	"fmt"
 	"regexp"
 	"strings"
 )
@@ -20,6 +21,13 @@ func rewriteFile(file ShoutFile, results []CommandResult, originalContent string
 			output = append(output, line)
 
 			if cmdIdx >= len(file.Commands) || cmdIdx >= len(results) {
+				// Out of bounds — skip past expected output, preserving original lines
+				j := i + 1
+				for j < len(lines) && !strings.HasPrefix(lines[j], "$ ") {
+					j++
+				}
+				output = append(output, lines[i+1:j]...)
+				i = j - 1
 				cmdIdx++
 				continue
 			}
@@ -62,6 +70,10 @@ func rewriteFile(file ShoutFile, results []CommandResult, originalContent string
 				output = append(output, result.Actual...)
 				if oldExitMarker != "" {
 					output = append(output, oldExitMarker)
+				} 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 marker to prevent parser from consuming it as one.
+					output = append(output, fmt.Sprintf("[%d]", result.ExitCode))
 				}
 				for k := 0; k < trailingBlanks; k++ {
 					output = append(output, "")