I did a yum update, and my webserver stopped working. The /etc/lighttpd/lighttpd.conf had its document root changed. (I set mine to serve from /srv instead of /var). Also, more annoying, the upgrade deleted the index.html from my document root. Luckily I keep my /etc and /srv in git, so I was able to revert them with git diff | patch -p1 -R
I think your setup stopped working because you hadn't edited the default configuration. It was set up to serve from /srv at one point, unfortunately this isn't FHS compliant from what I've understood, so it was switched back to /var/www instead. Your other issue raises an interesting point, though : Should the default index.html file be marked as %config in the package? I never thought of it, since I always point virtual hosts to other directories, never touching the original default directory, and I can only assume that most others do the same since this is the first time this problem is reported. Technically, that file isn't a configuration file, though... maybe another option would be to do something similar to the apache package, where there is no default index file, but the 404 error page for "/" is redirected to a special default page. This might mean having to enable some more modules by default, though.
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I've now tagged the default index.html as %config, so that even when the upgrade replaces it, the changed/replaced content won't be lost. This is the best I could come up with, the second best being including a README next to the default files, stating not to change them but instead create other directories beside the default lighttpd one inside /var/www/.