AppHarbor currently only supports deploying a single application from any repository. One option would be to dump the API into a web project. I did this for a WCF service without a web service here .
Another option is to support two AppHarbor applications and use the solution files according to which application you want to deploy for this application. That is, OurApp.Web.sln contains a web project and any supporting projects, and OurApp.Api.sln refers to the API project and any supporting projects. Learn more about the AppHarbor Solution File Agreement .
(disclaimer, I am co-founder of AppHarbor)
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