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I am assuming that you are using Cpanel on the host for the site. Just add the second domain as an addon domain. Because of the way that things are set up in Cpanel and the way it handles redirects, the crawlers will not realize the local directory structure that one site is sitting in the sub folder of another site. They will be viewed as if they are two different sites on different servers. So you would handle the robtos.txt like they were on two different servers and just disregard anything about one being in the sub folder of another.