@jakemkc I constantly find myself getting frustrated by the same search limitation in DEVONthink (re: need to search the contents of multiple groups or databases at once, but also need to exclude some groups or databases from the search).
At the moment, unless you rely on some other point of demarcation - like a tag or specific piece of metadata that you can use to exclude or include things - DEVONthink’s database/group-based searches are pretty limited. As someone that’s new to DEVONthink, this has always surprised me - especially given how fantastic its search is in other regards.
Until it’s addressed by DEVONthink, you might consider checking out the app HoudahSpot? I also find myself occasionally relying on Alfred’s search filters to get around this limitation in DEVONthink.
@rkaplan Frankly, you shouldn’t have to use HoudahSpot to do this; this really should be feasible in DEVONthink
In any case, I think your mileage will vary with HoudahSpot when being used to search for stuff in DEVONthink (though it’s great for everything else). For me, it’s very easy to search in a complex manner by groups because DEVONthink is mostly indexing Finder, meaning that I can just use HoudahSpot’s “Location” dropdowns to add/subtract whatever I want because my groups correspond to external folders in Finder. I also sometimes use HoudahSpot’s DEVONthink “Database” search to drill down on different combinations of database searches that DEVONthink cannot currently do (e.g., searching 3 of 5 databases, etc.).
I’m not sure if it’s helpful for you, but from what I can tell, these are the DEVONthink-specific column attributes that you can add to HoudahSpot (though you can add columns and search by whatever metadata you see in the file’s info panel):