SmartGroups are great, but they have a limited range of file types. A number of fora discuss Skim Notes. These notes, and only notes, would be searchable, if a SmartGroup could be created specifying the “kind” “is” “Skim”.
A workaround is to use “name” is “.skim”, but one can’t otherwise use that in the filename.
Please consider adding this simple feature that will make Skim Notes very searchable without getting all the original PDFs. It allows a user to search only the important stuff.
Another possibility would be for Skim to add a specified folder into which to backup its notes, but 1.3.9 does not have this feature. That folder could be indexed by DevonThink.