Use Github pages on multiple repositories when one has a custom CNAME already?
<p>I have a Github repository set up to host a small static site. The repository that hosts this is in the following format:</p>

<pre><code>username.github.io
</code></pre>

<p>This repository is setup to use a <a href="https://help.github.com/articles/using-a-custom-domain-with-github-pages/" rel="nofollow">custom domain</a> and has a CNAME file to do so properly. This repository works exactly as expected.</p>

<p>Now I want to set up a <a href="https://help.github.com/articles/user-organization-and-project-pages/" rel="nofollow">project page</a> and utilize the <code>gh-pages</code> branch for a different repository. When I do this, though, the CNAME in the first repository seems to apply and I am redirected to <code>example.com/REPOSITORYNAME</code> instead of using the expected <code>username.github.io/projectname</code> associated with this separate repository.</p>

<hr>

<p>How can I continue to use the <code>username.github.io</code> repository with a custom domain <em>and</em> the <code>gh-pages</code> branch on a different repository without redirecting the <code>gh-pages</code> repository to the custom domain defined in the first repository?</p>