My web server runs in a chroot jail. This makes things interesting because the paths are slightly different depending on whether you are inside or outside the chroot.

To override an incorrectly guessed path, I set setupconf in the .setup file. I also set allow_symlinks_before_srcdir=>1. However, when I tried websetup, the setup file was correctly changed but these important settings disappeared. This seems like a bug.

> I don't know what "setupconf" is. This is the first mention of it in the
> ikiwiki source tree. 
> 
> I've fixed the `allow_symlinks_before_srcdir` issue. --[[Joey]]

I meant setupfile as in IkiWiki::Setup::dump($config{setupfile}) from IkiWiki/Plugin/websetup.pm

Sorry for the confusion.