You definitely don’t “need to keep the DEVONthink Pro 2 folder to run DEVONthink 3”.
As @kfast mentioned, if you have some custom resources (templates, scripts, etc.) you’ve added, you’d need to migrate those manually. Otherwise, here is the current list for a full uninstall…
To do a deeper clean when moving from DEVONthink Pro (Office) 2 to DEVONthink 3…
Note: While it is not a prerequisite, we strongly recommend making sure your proper primary backups are current before starting this process.
Trash the following files and folders, noting the tilde (~) signifies the User Library:
- DEVONthink Pro (Office) application
~/Library/Application Support/DEVONthink Pro 2~/Library/Preferences/com.devon-technologies.thinkpro2.*- All DEVONthink Pro Office-specific scripts in
~/ Library/Scripts/ - All DEVONthink Pro Office-specific workflows in
~/Library/Workflows/ - All DEVONthink Pro Office-specific scripts in
~/ Library/PDF Services/ - DEVONthink related Bookmarklets from your web browser
- The Inbox in the sidebar of your Finder windows
- Delete the DEVONthink Sorter from System Preferences > Users & Groups > Login Items , if present.
Then reboot the machine.