Many (all?) links are pointing to github.com instead of github.io, which means they end up as 404's.
From a quick search it looks like the issue is that most links are absolute instead of relative, and so they're not reliable when hosted at a different domain. For example:
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<li><a href="http://net-ssh.github.com/ssh/v1/index.html">Net::SSH version 1.x</a></li> |
Related: net-ssh/net-sftp#127