Oh, I now get the issue you experience. I don’t ever see this with my LaTeX folders as I only put the compiled document (even if a draft) resulting from my writings into DEVONthink. Never felt the need to do much work in DEVONthink through the whole LaTeX folder/file structure. I try to avoid cluttering up DEVONthink with unneeded stuff–but being the packrat that I am, it’s difficult. If I had need to search a LaTeX project files I’d use a search tool (Spotlight, EasyFind, or something else).