- 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/TclCommandSetPath.py

@@ -89,6 +89,6 @@ class TclCommandSetPath(TclCommand):
 
         cd_command = 'cd %s' % path
         self.app.shell.exec_command(cd_command, no_echo=False)
-        self.app.defaults["global_tcl_path"] = str(path)
+        self.app.options["global_tcl_path"] = str(path)
         msg = '[success] %s: %s' % ("Relative path set to", str(path))
         self.app.inform_shell.emit(msg)