Assure Popup Windows (override-redirect) open over parent

The problem and solution is reported by `vx-sec` on  Github. It was
found on Xmonad WM. The fix simply raises the override-redirect window
to top, flushes display events and the restack windows for "Keep-on-top"
windows to work properly

Also tested on the default XFCE on r4.3

resolves: QubesOS/qubes-issues#9935

Author: alimirjamali

gui-daemon/xside.c

@@ -3466,6 +3466,10 @@ static void handle_map(Ghandles * g, struct windowdata *vm_window)
     (void) XMapWindow(g->display, vm_window->local_winid);
 
     if (vm_window->override_redirect) {
+        // Ensure override redirect window is raised after mapping
+        XRaiseWindow(g->display, vm_window->local_winid);
+        XFlush(g->display);  // Ensure raise takes effect immediately
+        // Then, if there are "keep on top" windows, move them to top
         restack_windows(g, vm_window);
     }
 }