This is actually a good question. And Jan just reminds me that i never explained that. So here we go:
First of all you need a mod_magnet, obviously. =) As second step you need to add mod_magnet to the server.modules array. Make sure mod_magnet is loaded before mod_fastcgi/mod_scgi/mod_cgi/mod_proxy/mod_proxy_core(1.5.x-snapshots).
Last but not least you can add this line to your lighttpd.conf:magnet.attract-physical-path-to = ( "/etc/lighttpd/cleanurl-v5.lua" )
