I don’t think there is enough here to make a full page on the differences between a directory and a repository. Directory = lists/indexes content, repository = hosts content. That’s pretty much it.
If we do need to have more discussion about this, then a forum thread in the plugin directory subforum is the right place. (Edit, I’ve moved these posts over to the right place, feel free to discuss here.)
I’m writing a blog post now about the current status of ClassicPress development and I will include a note about this distinction there.
This will come along with the implementation of the directory.