Improve tray manager handling, particularly on macOS #1825

* On shutdown, message tray manager before lengthy project shutdown
* When dead ports are found, explicitly update the menu

src/serena/agent.py

@@ -1472,10 +1472,7 @@ class SerenaAgent:
         Shutdown handler of the agent, freeing resources and stopping background tasks.
         """
         log.info("SerenaAgent is shutting down ...")
-        if self._active_project is not None:
-            log.info(f"Shutting down active project '{self._active_project.project_name}' ...")
-            self._active_project.shutdown(timeout=timeout)
-            self._active_project = None
+        # apply shutdown depending on allocated resources, handling quick ones first (dashboard manager & GUI viewer)
         if self._gui_log_viewer:
             log.info("Stopping the GUI log window ...")
             self._gui_log_viewer.stop()
@@ -1483,6 +1480,10 @@ class SerenaAgent:
         if self._dashboard_manager:
             self._dashboard_manager.shutdown()
             self._dashboard_manager = None
+        if self._active_project is not None:
+            log.info(f"Shutting down active project '{self._active_project.project_name}' ...")
+            self._active_project.shutdown(timeout=timeout)
+            self._active_project = None
 
     def shutdown(self) -> None:
         """

src/serena/dashboard.py

@@ -1155,6 +1155,7 @@ class SerenaDashboardTrayManager:
                         for port in dead_ports:
                             self._instances.pop(port, None)
                             log.info("Removed unreachable instance on port %d", port)
+                    self._update_menu()
 
                 # terminate if no instances remain
                 with self._lock: