Why Can't I Transfer Folders with Files

I was hoping to use my new Ipad as a reader for a research library of over 5,000+ pdf documents that I have accumulated for my research into the Camp Lejeune drinking water contamination. Sadly, I found I could transfer files but not folders in which I have my files organized. Anyone have any ideas or suggestions. The App developers I have contacted say the problem is in Itunes and Apple says it is the Apps themselves.
Any ideas would be appreciated.

There are two parts to what you're trying to do-
First, you need an iPad app that supports folders- Apple's iBooks app does not; PDF Expert by Readdle (the best PDF app I've found so far, $4.99) does allow folders.
Second, you need a Computer (Mac/PC) app that allows you to sync folders Computer-to-iPad. iTunes file sharing does not allow this. However, there are third-party solutions that allow this, without jailbreaking your iPad. The best one I've found is PadSync by Ecamm. ($10)
Send a request to Apple also: www.apple.com/feedback

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