Warning: Permanently added the RSA host key for IP address '204.232.175.90' to the list of known hosts.

Github.comが、サーバ増強に伴いIPアドレスを増やしたそうです。
Additional IP for GitHub.com
Soon, we will begin using additional IP addresses (A records) for GitHub.com in order to add more load balancers.

Starting Thursday, April 4, 2013, GitHub.com will also resolve to 204.232.175.90, in addition to the current IP (207.97.227.239). Both addresses resolve to GitHub.com via reverse DNS.

If you are using SSH, you will see this message the first time you see this IP address:

Warning: Permanently added the RSA host key for IP address '204.232.175.90' to the list of known hosts.
This warning is the expected behavior of SSH clients.
Upcoming IP address changes

このWarningはSSHクライアントの想定内の振る舞いなので心配しないでください、ということですね。
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