- 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
- Drilling Tool - working in adding tools auto-load from Tools DB
- some updates to the Excellon Object options
- Drilling Tool - manual add from Tools DB is working
- fixed the issue with factory_defaults being saved every time the app start
- fixed the preferences not being saved to a file when the Save button is pressed in Edit -> Preferences
- fixed and updated the Transform Tools in the Editors