I also think it makes more sense to store this in our git. Specailly now that it's a young project.
Everything with the same version system makes much more sense.
Also, I find the addition of MediaWiki 1.18.1 in r5 quite confusing. That's not what was.
I'd make a branch of wikiHow releases, another of patches to their base version (ie. how they evolved) and a new one of "improved version for wikiHow", which would be a merge of recent MediaWiki with their patches.
I'm not sure about the best way to handle their extensions, though. Maybe by replicating the same approach with a repository per extension.
Currently, diff -ur wikihow-src wikihow-read-only/wikiHow/ contains lots of unrelated changes. How is one expected to make sense of it?