Hi, I've just managed to send off an IPA from Stencyl 2.2 using this method. Let me try to remember whatI did...
In Stencyl, test the game on iOS(Device) to open up the project in Xcode. Wait for it to load up.
Select AppScaffold in the left hand column.
In the middle part of the window, at the top, you have some options. "General - Capabilities - Info - Build Settings - ..."
Click on Build Settings.
Use the search bar (just below where you clicked on build settings) to find "Compiler for C/C++/Objective-C"
Change this option from unsupported to default as Vanz suggested.
Then use the search bar to find "Provisioning Profile" in Code Signing. Choose your correct Provisioning Profile for what you want to do (Whether you want to submit to App Store/Ad Hoc)
Now, back at the top of the window next to the play/stop buttons it says Appscaffold > iPad > iOS 7.0
Click and hold on iPad to change it to iOS device.
In your taskbar click on Product > Archive. Wait for it to cook and in the window that pops up next click Distribute. Choose the one you want to do and you're on your own from here!
Submit to the iOS App store is the option I just chose, and it delivered the app to iTunes connect without going through Application Loader, which strikes me as a bit odd. My app is waiting for review, so I'll let you know what they say!
Oh, also there were these two warnings with the app - it's not fatal I guess, I'll let you know how it goes!
