The idea was to introduce $wgDeletedDirectory to the core, and to stop using $wgFileStore['deleted']. Installer variables just have identifiers as names and don't set array members, and $wgFileStore is obsolete anyway, existing only to set that one directory.
I like the idea of doing that, but right now it's just throwing a notice on each page, that was my main reason for removing it. I can re-add it commented out though.