Those are different names.
I think they are the same human-word. I have $wgCapitalLinks set ;) I don't see the point of having that two folders separated. The contents are on different subfolders so no problems would came from there. Maybe links to the repository? I don't think it's being very linked. And most references to the moved folder would be handled by the subversion merge feature.
Don't check out the entire repo, that's a waste of time, disk space, etc. Check out specific bits.
It's not something very likely, but the repo _is going to fail_ for somebody with an uncommon config. If we were going to only accept valid input most of the parser work wouldn't be necesary and this maillist wouldn't be full of 'MediaWiki automated test run failure's.