Use _stop_event consistently across all threads as the way to signal that it should stop. Add thread joins with timeouts to allow the program to exit cleanly

core/cleanup.py

@@ -34,6 +34,10 @@ class CleanupTimer:
         """Stop any threads and prepare for application shutdown"""
 
         self._stop_event.set()
+        if self._thread:
+            self._thread.join(timeout=15)
+            if self._thread.is_alive():
+                logger.warning("Cleanup worker thread did not exit on time and will be killed.")
 
     def _run(self):
         while not self._stop_event.wait(timeout=self._cleanup_interval):