The removal of the App Store comes with the update to version 12.7 of the software, which Apple launched in the wake of yesterday's big iPhone X announcement. If you have an iOS app, ringtone, or book that's no longer available, you can move that to your iOS device while plugged in to a computer with a USB cable, as long as it's still on your computer.
Just like the previous major iOS updates, you will be able to install the iOS 11 update on your iPhone or iPad wirelessly by downloading the OTA update directly on the device. That was a simple case with the iPods but when the iPhone and iPads arrived, Apple decided not to have a separate app management software and repurposed iTunes instead. Some users may have been used to managing apps and ringtones from the app, but pulling that section out could be part of a long-anticipated quest to solve the bloated, sprawling mess that Apple's desktop music app has become. People will also be more likely to use the redesigned App Store coming in iOS 11.
Now it might look like the bad guy for yanking out the app section, but it's all for the goal of keeping iTunes focused on entertainment content.
With the iTunes version 12.7 for both Windows and macOS, quietly released during the keynote event in Cupertino, you no longer have access to the App Store on desktop as the focus is now on "music, movies, TV shows, podcasts, and audiobooks".
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The iOS 11 will include a new app called Files, which will allow users to manage documents stored in the device.
iOS 11 was first announced at this year's WWDC and has been in the hands of those on Apple's beta program for some months now.
There are other changes to other types of content too, but not as disruptive as this. iTunes U, for example, has been moved to the Podcasts section.