Just so that I get this right form the beginning this time:
cmake should create the normal "resources.cfg" for the devs and another one (resource.cfg.zip) that your install script can copy and rename to "resource.cfg" for the release version?
About zipping the other files:
The graphics can be zipped because Ogre officially supports zipped files natively. SFML doesn't support this afaik. CEGUI uses some parts of Ogre, but I'm not sure if it uses the resource manager (zipping only works with the Ogre resource manager). But the gui files are the quickest to load anyways.
There are two other reason besides zip support:
1) SFML only loads the sound/music files when they are needed. But Ogre parses all the graphics files directly at the start (better to only load one small zip instead of 100 big text files from the slow HDD). It won't make a difference with single audio files.
2) Zipping sound and music wouldn't decrease the files size, too (ogg is compressed already).
Basically it would be possible if we code our own routines or somehow connect SFML with the Ogre resource manager or something alike, but I think that wouldn't bring any performance increase. Most important are the graphics.
edit: Just pushed a commit with an updated README file (updated the build instructions and added section about folder structure) and removed the TODO.txt (last update to it was in February, and we should better use trac or in-source TODOs for this, most of it is probably already fixed or already in-source TODOs anyways).
I think there's not much left to do with the folder stucture. It's very clean now, easy extendible and documented directly on the repo.
