When I am using Application Loader to upload the app binary to the Apple do I submit a .zip file of my whole application or the .ipa file. I am confused about this process.
For iOS applications you just need to submit a zipped .app, the same .app generated by Xcode is enough, no need to put it into an IPA before archiving it.
For Mac OS X applications (Mac App Store), you need to submit the PKG generated by Xcode's Organizer Share/Save To Disk… command.
Alternatively, you can use the Build And Archive command and submit via the Xcode Organizer window… as another user points out.
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