Add copy on source directory configuration to gh-pages deployment page

Funny, I thought this went in the master branch, but on the page I was editing it indicates that you keep the site in the gh-pages branch, so I confused the two with the initial request.

From issue #2648 I thought it would be helpful to mention on the gh-pages deployment page that a site's source files must reside in the root directory.

note:
- used "warning" flag.
- pointed to relevant troubleshooting page on gh-pages docs as well as jekyll docs on configuration variables.
- placement doesn't seem critical. Can be at the bottom of the page.
Why not make this the warning? Why warn the thing above?