Hi John,
I think folder structure is the root cause.
I noticed that after retrieving the standard Fiori application, the objects like application.json, Main.view.html, Main.controller.js etcetera and all the folders i18n, css, view and more are put directly under the root of the project and not under the WebContent folder.
Please refer this document. How to Guide: SAP Fiori Extensibility - Addind Custom Fields in UI
Regards,
Masa
SAP Rapid Innovation Group - RIG