Don't recall anything about shell scripts. I remember configuring some crazy-formatted .xml file for mail parser and then setup a cron job to run some kind of cerberus-2.649.Linux-2.4.18-3smp binary pointing it to the .xml file where all the information about POP3 server was provided.
Kayako might be confusing in the beginning but it seems to be working well for us except one thing - live chat - very resource intensive and has number of critical (at least for us) bugs, so we disabled Kayako live chat and switched back to websitealive. Almost no complains about how Kayako handles tickets / KB / tasks scheduling. Also, Kayako offers online demo - try to signup for demo account and take a look at admin control panel - pretty much all configuration, customization, etc is done through the web interface in Kayako.
Regards,
Paul