@jprint In order to open files in my DEVONthink index and prevent the MarginNote database from reimporting a copy of the same file (another limitation of MarginNote in general: There’s no checking for duplicates when opening outside of MarginNote.), I use a Keyboard Maestro automation script to write lock directories while MarginNote is open and unlock them while MarginNote is closed (During this time, you can import new files in DEVONthink.). The script I have is outlined here: Allow Opening From ~/Library/Containers/QReader.MarginStudyMac/Data/Documents/ Without Reimport
This way, I can open files in DEVONthink directly from the ~/Library/Containers/QReader.MarginStudyMac/Data/Documents/ directory with expected behavior. This system works pretty well. It’s not ideal, but it’s a decent hack until the development team implements better database structures, import logic, and file browser user interfaces.