Properly close main window in fixture

This mirrors the changes in PR spyder-ide/spyder#21353

spyder_unittest/tests/conftest.py

@@ -41,16 +41,15 @@ def main_window(monkeypatch):
     CONF.set('tours', 'show_tour_message', False)
     QApplication.processEvents()
 
-    # Reset global state
-    dependencies.DEPENDENCIES = []
-    PLUGIN_REGISTRY.reset()
-
     # Start the window
     window = start.main()
     QApplication.processEvents()
 
     yield window
 
     # Close main window
+    window.closing(close_immediately=True)
     window.close()
     CONF.reset_to_defaults(notification=False)
+    CONF.reset_manager()
+    PLUGIN_REGISTRY.reset()