The function interwiki_filter contains some code to handle http, https, mailto and ftp links differently. I had to patch this in order to make file links work. I changed
if (preg_match("/^(http|https|mailto|ftp):/i", $url)) {
to
if (preg_match("/^(http|https|file|mailto|ftp):/i", $url)) {
It would be great if this could be added to the standard distribution.