Problem crawling MediaWiki with Search Server / Sharepoint
Fragment of a discussion from Project:Support desk
That'd be odd for internal links to have rel=nofollow. (by default external links have that - $wgNoFollowLinks, but internal links shouldn't. You can manually cause things to be not indexed using $wgArticleRobotPolicies or __NOINDEX__ but that's usually not something done without meaning to).
Since you mentioned special pages not working for you because they're noindex - have you tried just creating a new wiki page with only {{special:prefixindex}} on it and pointing the spider at that?
