- 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/TclCommandGetSys.py

@@ -55,7 +55,7 @@ class TclCommandGetSys(TclCommand):
 
         name = args['name']
 
-        if name in self.app.defaults:
-            return self.app.defaults[name]
+        if name in self.app.options:
+            return self.app.options[name]
         else:
             return "The keyword: %s does not exist as a parameter" % str(name)