Apple changed file permissions starting in iOS 6 to where the app bundle or .app (dot app) subdirectory of an app is now read-only (and even hidden in iOS 8-10) which means you can no longer modify its contents (add, edit, or replace files), but you can still access files in the Documents and Library subfolders (depending on your iOS version). We are looking into any way around this Apple restriction, but so far, the only way to gain full access to the .app folder is via Jailbreak (hacking iOS and gaining root access). Since it's a file permissions issue, all other iOS transfer utilities will have the same issue and either not display the folder or have the same or similar access in iOS 6-10. Basically, the more recent your iOS version, the less access you have due to Apple trying to take more control and stop customization of apps among other reasons.
In iOS 8 and 9, Apple locked it down even more and made the folder into a symlink (alias/shortcut) for a root directory which can't even be read, so the only way to access the app bundle in iOS 8-10 is if you Jailbreak your iPhone, iPad, or iPod Touch.
There is an iOS 7 Jailbreak for iOS 7.0-7.0.6 devices called evasi0n which you can find out more about here: http://evasi0n.com. Or, if you are running iOS 7.1 or later or iOS 8.0 - 8.1, then you'll find the Jailbreak here: http://pangu.io. For iOS 8.1.2, you'll need this one: www.taig.com/
Once you Jailbreak your iPhone, iPad or iPod Touch, you’ll then be able to gain full access to that folder and make any file changes you want. If you also install afc2add (or Apple File Conduit "2") from the Cydia app store, you’ll even be able to access the root (/) folder of iOS.