I assume that you are building with Phonegap Build from your GitHub account.
In that case, the Developer App was a bad start, since it isn't compatible with PGB.
Phonegap Build requires your assets and a config file only, where both index.html and config.xml should be in the root of your repo, and no cordova.js or phonegap.js file should be present in your assets.
Also, from the developer app, you may be using old, deprecated plugins from pgb instead of the latest versions of them from npm.
See the Phonegap Build Docs.