I have developed 3 iPad single window applications and my apps were rejected in app store because they belong to an organization. I have been searching solutions for publishing these apps in app store without distributing them through ad-hoc distribution. I came across some solutions like enterprise app development and having a username and password for the app. I decided go with the second option and I am unable to find any solution on how to set up username and password for this single window app, so that I can submit the apps to app store and our organization people can download it whenever they want.
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Create an entry for the username and password. When the user submits it, you can check the input against PHP or another online method. Save the username and password to the keychain and repeat this each time the app starts.