"Flatten" index for DTPO?

Hi, everyone!
I’m working on some academic research, and I’ve been using Papers 3 for searching & collecting citations. I also need to use DTPO’s AI to classifying the contexts. I achieve this by using DTPO to index the Papers 3 library on my disk. But the problem is, the Papers library has its own organization structure and it uses nested folders to store the PDFs. So when I want to access a PDF file in DTPO, I need to traverse through the nested folders until I finally find that file I want. I guess that is also decreasing the efficiency of indexing. So my question is, is there a “flatten” mode that allows me to index only the PDFs in the Papers library that omits the folders structure? Any suggestions is welcomed!

No. Indexing includes the full contents of the Finder folders. However, just add a Smart Group with criteria Kind is PDF/PS and point it at the folder.

Thanks! Exactly what I want!