Journey to robust Windows Services: Overriding the default web site when deploying your applications from the command line

I recently ran into a problem where I wanted to deploy a new application to the default web site on an old IIS 6 instance via MSDeploy on the command line from my build machine. Unfortunately, it decided to deploy the application in a folder immediately underneath the default web site, rather than as the default website itself. This post on the IIS forums provided the solution.