As of Rev. 163 originals are announced along with a file as soon as a file with an identical name shows up within a given subfolder of the images own folder. This is a _very nice_ feature, indeed.
However, it seems advisable to split derived files and original files in their directory structure, instead of using subfolders within the original files. E.g. a file structure like this might come to mind (R for Raw, though it doesn't impose to be NEF, could also be JPG):
In my current workflow I split the R* folders such, that they are compatible with my "offline backup medium", say ~4GB for a DVD Rom, while I keep shootings together.
In postprocessing one might come up with derived files like
A splitting like this would greatly reduce the risk of accidentially working on the original files instead of derived copies (most critical in a JPG workflow), it simplify offline backup strategies like the one outlined above and makes it easy to dump down a "client copy" of the images by using the D/ structure.
Currently, I do it by hand, though as the "originals" folder goes right into some automatisation of this process, I'd like to suggest it here. So if Mapivi could come up with path handling like "Target Folder fixed part" and "variable part" as it's done in the import wizard for this cross checking one would already be there.
BTW: This directory layout is heavily inspired by Kroghs "DAM Book" (http://gso.gbv.de/DB=2.1/PPNSET?PPN=581078365, or for the German edition http://gso.gbv.de/DB=2.1/PPNSET?PPN=523589875\). Though he's always talking about quite expensive commercial tools Mapivi makes a very good substitute in many places. IMHO the main difficulty is currently the integration of "real raw". (Feaseble though as well.)