The Phonegap Developer app has been removed from the App Store due to Apple developer constraints.
What will this mean for us deving for iOS and using Phonegap to add native features? Will apps build with Phonegap be rejected?
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As indicated in the conversation you linked, this is a specific case due to a bad usage of a QR Code.
The app will likely even go back up at some point.
It's just a developer utility for Phonegap, even if it's permanently removed I don't think it would affect anything else in Phonegap or Cordova.