I updated to 1.3.19 (456) and no plugins and scripts appear in the appropriate menus.
1.3.19 (456) here
All my plugins and scripts are there as they should be.
I think this was a weird Mac OS bug. My entire Glyphs directory was somehow moved to ~/Library/Containers/com.schriftgestaltung.glyphs/Data/Library/Application Support
This happens when you run an App Store version of the app. The it migrates the application support folder info the sandbox.
Yes, I ran the app store version when I was testing that font generation bug in 1.3.18. Thanks!