Help me understand the underlying iPAD file system

The underlying filesystem on the iPad is the standard OS X filesystem. In the iPad model, each application is a separate user and has it's own directory. In that directory, all of the application files are read-only, save for a single folder for user data. If you upgrade an application, the application data in the app directory is replaced, but the user data preserved. An application can only access files in it's home directory, and nowhere else.

Applications cannot access each other's directories at all. If you do an "Open In..." in an application, it's calling on an iOS service that copies the file from one application's data directory to the other's. There's no notion of sharing files (though, the core databases of Photos and Contacts can be accessed through a service and an application can refer to a photo or contact by a unique ID), except by copying them. It's up to the application whether or not it stores the file it receives temporarily or for an extended period of time. The implication of this model is also that deleting an app also deletes all the app's data and settings.

The fundamental difference between the desktop approach and the iPhone/iPad approach is that on the Desktop, information is associated with a user, whereas in iOS it's associated with and application. The iOS approach makes it impossible for applications to interfere with each other at the filesystem level, and it is one piece of the iOS security model.

I cannot explain the file system well. To me, it remains one of the fundamental differences between the windows approach and anything apple makes.

But there are a couple of tools. If you are looking for space hogs, go to settings, usage. When you give it a minute, it will list all of you apps and their size. If you tap an app, it will then show you the documents and media associated with that app. ( the size, not the individual components). So if your docs to go library starts to get out of hand, you will be able to see it.

For a full peek at the file system, find and download a program call iexplorer onto you computer. When you plug the pad in, a windows explorer type window pops up that shows all. But dont horse with it unless you are real clear about what you are doing. There are versions of this available for both mac and windows.

With regard to Safari, if you want to clear it, you can delete the cookies and cache in the settings if you want to do so - if that helps at all.

Go to Settings>Safari>Clear History, Cookies and Data.

I thought you could delete stuff in goodreader from the pad? Out of curiosity, what happens if you open them in i books as opposed to good reader? Can you delete them there? If so, when yo do sync, make sure they are 'unchecked' or deleted from i tunes, or they will get reloaded during the sync.

I don't quite understand your issue, as what you're describing happens pretty much exactly the same way in the 'normal' world also.

1. I download a file using Safari, or whatever, and it now resides on my Desktop.
2. I open that file in Pages, edit and/or just save it ... it's now in Documents as a Pages file
3. I open the original file in NeoOFfice, edit abd/or just save it ... another file in Documents as a .doc file
4. and etc.

The iPad and iOS actually has no file handling system at all, no equivalent to Finder or Explorer. Everything is handled within apps, as you've noticed. You do point out that deleting a file in one app won't delete it in another app; I have no idea why you would want that to happen in most cases, and can think of all sorts of reasons why the OS would block off App A from playing around with the contents of App B.

Your final point is just semantics, a distinction which you no longer need now that you've understood it and one which, well, few if any others have ever had any issues with. If you're concerned enough about it you should contact Apple directly via their Feedback links and make your best case to them.