Some recipes add extra functions that make changes to the source, e.g. meta/recipes-devtools/dmidecode/dmidecode_2.12.bb; it may be nice to track these as commits in the resulting git repository where possible rather than having them potentially get mixed in with other patches or remain uncommitted at the end. (The logic for this is in GitApplyTree in meta/lib/oe/patch.py and is invoked via do_patch in patch.bbclass.) The changes might be done in a task added after do_unpack or do_patch. If we do implement this we will need to ensure this doesn't disrupt update-recipe, i.e. any commits we make would need to be marked in a similar way we mark commits from patches, and update-recipe would need to ignore those marked commits.
AFAIU, it would be enough to track any extra changes between do_unpack() and do_patch(). That shouldn't be to hard as we're already executing the extra steps (if any). We'd just need to run them one at a time and commit possible changes to git. With certain meta tag or some other means to prevent patch creation from those commits, of course.
Indeed, that's what I was thinking. It's just a matter of implementing it.
Fix merged to master: http://git.yoctoproject.org/cgit/cgit.cgi/poky/commit/?id=ddfe74447b3a50ae0b3533ace0e2b41e04a57bff