In attempt to solve and debug the issue, we created a brand new build.phonegap project, and created a new branch on github and removed ALL 'gap:plugin' and 'plugin' tags from config.xml
The build was successful, and the 'plugins' tab showed one plugin: 'cordova-plugin-secure-storage' which appeared even when we didn't have any plugins in the config.
next, we re-added all of the plugins to config.xml, except for phonegap-plugin-push and rebuild the app.
this build was successful, but the 'plugins' tab on the app didn't have any plugins listed even when many plugins should be included.
Note: this is the code that always build successfully for many weeks prior to 2 days ago when the issue started happening.
the config.xml wasn't modified for several weeks prior to this.
Are you zipping up and uploading an entire cordova application? If so, you shouldn't be -- just upload the www folder with a config.xml. Alternatively run phonegap remote build ios, which should upload the correct files.
When you upload an entire phonegap / cordova app directory, you are uploading the platforms directory which has platform config.xml files which can cause confustion to the build system. If you haven't run phonegap prepare those files may still include your old plugins.