- 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/TclCommandGetPath.py

@@ -61,5 +61,5 @@ class TclCommandGetPath(TclCommand):
         """
 
         self.app.shell.append_output("Current default Tcl Shell path is: ")
-        path = self.app.defaults["global_tcl_path"]
+        path = self.app.options["global_tcl_path"]
         return path