You can clone with
HTTPS or Subversion.
An epub file is actually a zip with a special point: the mimetype file must be the first, and it must NOT be compressed. This cannot be done afaIk with CodeIgniter Zip class.
I suggest to improve the Zip.read_file adding an optional parameter, boolean compress. If not set, it is true. If set to false, it would add the file without compressing it. Pear Archive_Zip can do it with something called ARCHIVE_ZIP_PARAM_NO_COMPRESSION
Can you see if my changes work with epubs? I only added compression options, I don't know what you meant by the mimetype being first.