Actually in the case of ecolcin.com your WordPress URL is http://portal.ecolcin.com not http://ecolcin.com/portal so this is not technically a subdirectory install. It may be that the site is installed inside a sub-directory that is inside public_html but WordPress does not see it that way. If you have a site that is in the root public_html directory then you can user that site to scan nall the other sites inside it.
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