It seems PhoneGap generates that file automatically when
Phonegap uses config.xml to create androidmanifest.xml when you add the android platform to a project. It is also modified when you add plugins and build the project (for example, it adds the required permission for the plugin).
But you can also manually edit the file in
platforms/android/AndroidManifest.xml to add permissions, configure the activity or the application... it will not be lost when you rebuild your project.