Where do I set that Devonthink should delete files from the database (from the ‘files’ directory in the package) when I choose to delete an item?
Now all the files remain there: I see files there which I deleted months ago, still present in that files directory, but no longer visible in the Devonthink application.
That should not be the case. Generally, the newest versions of DEVONthink delete also the files in the Files folder. Maybe in your case these files are remainders of earlier versions.