I think I can see your problem. Your migrations (and I assume also the schemas) sit in the _web app. And, apparently, you used the new mix phx.new --umbrella generator that generates the main app, and _web app.
I think you ran the mix phx.gen.schema inside _web app. Which generated the files there. But this _web app has no Repo. Repo is inside the other, main app.
Unfortunately, the mix phx.gen.schema does not seem to work from within the main app (I think it probably will in final veersion of Phoenix 1.3). Which probably leaves you with only option to move the migrations and schema files to the main application, from _web application
