By default, Jekyll is used to process GitHub pages. Files / directories beginning with underscores are of particular importance to Jekyll, and therefore they are handled differently.
Since you don't seem to be using Jekyll, your easiest solution is to add a file named .nojekyll to the root path to disable Jekyll functionality.
For more information contact https://help.github.com/articles/files-that-start-with-an-underscore-are-missing/ .
Edit: To be clear, the intruder directory is "_include".
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