Ipad, filing, folders, opening a document with more than one app...

Hi
I am wondering about iPad filing, documents and the future that iOS 5 and iCloud hold.
Am I right in thinking that there will still be no file/folder structure and that documents will be held individually by apps?
This creates two problems for me:
1)  I need to access the same document (e.g. a pdf file) from more than one app. For example, say I need to use iAnnotate to mark it up and Sente to file it. However each app keeps their own copy of the document, so the annotated copy from iAnnotate is not the same copy as the one filed correctly in the Sente database.
2) How do I keep the files for a specific project together? Say I have source documents, word-processing documents, presentations, images etc all related to one project: how do I keep them all together? If we had tagging  (as in openmeta or similar) I could tag them - works beautifully on the desktop but not available on the iPad. If we had folders I could at least group them in folders... What is is the iPad solution?
M

Here's how I address # 1:
I use DropBox as my central hub to keep documents accessible and synced between my iPad and my laptop. That means that I export, share, copy or print the document, with my changes, to DropBox from whatever application I'm using. For example, if I open a PDF in PDF Expert (the app I use for reading and annotating) I can "open" a copy in DropBox with my annotations. For Pages and other iWork files I use DropDAV which enables me to save to DropBox via WebDAV. For other apps like Safari that don't have DropBox integration, I use Save2PDF to "print" a PDF to the appropriate DropBox folder.
As to #2, two things come to mind. The first is that you can use the search function to find related files if you put your tag in the title or somewhere else searchable. The second is that I set up a file structure in DropBox on my laptop that meets my needs (and is also one way to begin to emulate a file structure on the iPad). For example, i keep my current course files, with their presentations, documents, and spreadsheets, in DropBox. But many of my projects have so many components and so many images, etc, I've become used to having components in different applications (Aperture, iTunes, etc) and I do rely on my laptop (and its external drives) for my central and final project management. For things in process, though, the iPad works very well.
ICloud may change all this. :-)

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