- the application now uses only the default values from the app.options dict, the app.defaults dict holds the definitive default values

- fixed some outstanding issues from the PyQt6 port
- PEP8 fixes
- minor fixes
- updated the saving of Preferences to update the self.options too: the `Apply` action will update the self.options but the `Save` action will save the updated preferences to the file on disk

tclCommands/TclCommandListSys.py

@@ -60,8 +60,8 @@ class TclCommandListSys(TclCommand):
         """
         if 'selection' in args:
             argument = args['selection']
-            return str([k for k in self.app.defaults.keys() if str(k).startswith(str(argument))])
+            return str([k for k in self.app.options.keys() if str(k).startswith(str(argument))])
         else:
-            ret_val = list(self.app.defaults.keys())
+            ret_val = list(self.app.options.keys())
             return str(ret_val)
-            # return str([*self.app.defaults])
+            # return str([*self.app.options])