I'll try it out in a bit. Couple thoughts on first inspection:
rdf/recent.phtml doesn't output HTML. ;) I recommend renaming it to rdf/recent.php. (And simply calling on it as /rdf/recent, thanks to the magic of Apache's MultiViews setting.)
maintenance/initialdata.sql has English text and password hashes hardwired into it, and everything that this file does is immediately replaced by populatedata() in install.php. Do we need it? And what's with the automatic creation of WikiSysop and WikiDeveloper accounts?
And of course the docs are still out of date. ;)
In general I do like the restructuring; the source dir was getting a bit cluttered. And at least in theory this should make it easier to share one copy of stuff among multiple installations.
-- brion vibber (brion @ pobox.com)