diff --git a/cmd/root/root.go b/cmd/root/root.go
index 9f2993396..c1f2ee1b2 100644
--- a/cmd/root/root.go
+++ b/cmd/root/root.go
@@ -204,25 +204,26 @@ func (e RuntimeError) Unwrap() error {
 	return e.Err
 }
 
-// isFirstRun checks if this is the first time cagent is being run
-// It creates a marker file in the user's config directory
+// isFirstRun checks if this is the first time cagent is being run.
+// It atomically creates a marker file in the user's config directory
+// using os.O_EXCL to avoid a race condition when multiple processes
+// start concurrently.
 func isFirstRun() bool {
 	configDir := paths.GetConfigDir()
 	markerFile := filepath.Join(configDir, ".cagent_first_run")
 
-	// Check if marker file exists
-	if _, err := os.Stat(markerFile); err == nil {
-		return false // File exists, not first run
-	}
-
-	// Create marker file to indicate this run has happened
+	// Ensure the config directory exists before trying to create the marker file
 	if err := os.MkdirAll(configDir, 0o755); err != nil {
-		return false // Can't create config dir, assume not first run
+		slog.Warn("Failed to create config directory for first run marker", "error", err)
+		return false
 	}
 
-	if err := os.WriteFile(markerFile, []byte(""), 0o644); err != nil {
-		return false // Can't create marker file, assume not first run
+	// Atomically create the marker file. If it already exists, OpenFile returns an error.
+	f, err := os.OpenFile(markerFile, os.O_RDWR|os.O_CREATE|os.O_EXCL, 0o644)
+	if err != nil {
+		return false // File already exists or other error, not first run
 	}
+	f.Close()
 
-	return true // Successfully created marker, this is first run
+	return true
 }
diff --git a/pkg/app/app.go b/pkg/app/app.go
index c49eed8b7..12893bea5 100644
--- a/pkg/app/app.go
+++ b/pkg/app/app.go
@@ -446,8 +446,18 @@ func (a *App) RunWithMessage(ctx context.Context, cancel context.CancelFunc, msg
 }
 
 func (a *App) RunBangCommand(ctx context.Context, command string) {
-	out, _ := exec.CommandContext(ctx, "/bin/sh", "-c", command).CombinedOutput()
-	a.events <- runtime.ShellOutput("$ " + command + "\n" + string(out))
+	command = strings.TrimSpace(command)
+	if command == "" {
+		a.events <- runtime.ShellOutput("Error: empty command")
+		return
+	}
+
+	out, err := exec.CommandContext(ctx, "/bin/sh", "-c", command).CombinedOutput()
+	output := "$ " + command + "\n" + string(out)
+	if err != nil && len(out) == 0 {
+		output = "$ " + command + "\nError: " + err.Error()
+	}
+	a.events <- runtime.ShellOutput(output)
 }
 
 func (a *App) Subscribe(ctx context.Context, program *tea.Program) {
diff --git a/pkg/tools/builtin/shell.go b/pkg/tools/builtin/shell.go
index 91978074d..83c1d2300 100644
--- a/pkg/tools/builtin/shell.go
+++ b/pkg/tools/builtin/shell.go
@@ -6,6 +6,7 @@ import (
 	"context"
 	"errors"
 	"fmt"
+	"log/slog"
 	"os"
 	"os/exec"
 	"runtime"
@@ -137,6 +138,10 @@ func statusToString(status int32) string {
 }
 
 func (h *shellHandler) RunShell(ctx context.Context, params RunShellArgs) (*tools.ToolCallResult, error) {
+	if strings.TrimSpace(params.Cmd) == "" {
+		return tools.ResultError("Error: empty command"), nil
+	}
+
 	timeout := h.timeout
 	if params.Timeout > 0 {
 		timeout = time.Duration(params.Timeout) * time.Second
@@ -152,6 +157,8 @@ func (h *shellHandler) RunShell(ctx context.Context, params RunShellArgs) (*tool
 		return h.sandbox.runCommand(timeoutCtx, ctx, params.Cmd, cwd, timeout), nil
 	}
 
+	slog.Debug("Executing native shell command", "command", params.Cmd, "cwd", cwd)
+
 	return h.runNativeCommand(timeoutCtx, ctx, params.Cmd, cwd, timeout), nil
 }