Maybe you could make the library hidden, e.g. ".libraryKOreader", or even put it in KOreader directory.
Then either you give reader.lua the directory as a starting directory by adding the path behind reader.lua in the script "koreader_kobo.sh".
Or you rename it before starting reader.lua to a sub of /mnt/onboard and before starting nickel to a hidden name. The script to use before nickel is "run.sh" (or etc/init.d/rcS see http://wiki.mobileread.com/wiki/Kobo...g_Telnet.2FFTP
) and the script before reader.lua is "koreader_kobo.sh".