I've started adding some documentation on chunked uploading via the API on mediawiki.org:
https://www.mediawiki.org/wiki/API:Upload#Chunked_uploading
This info is based on watching UploadWizard at work, and may be incomplete or misleading. :) So please feel free to hop in and help clean it up, thanks! There also probably needs to be better information about stashed uploads, which has some intersection with chunked (for instance -- is it possible to do chunked upload without using the stash? Or are they required together?)
-- brion