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Will future versions of OG apps for iPad be able to link to files created by other OG apps. For example I have links to quite a few OO files from the notes field in OF for Mac. Obviously these links aren't synced because they're not supported in OF iPad. Once OO iPad is released...will links of this type be supported? If I understand the Apple "rules" there would have to be some tweaking. All of the OG apps could be in a "container" app which would then make Apples rule moot.

I apologize if this has already been addressed...I didn't find it in my search.
First, a bit of nit-picking: the links (and attachments) are synced everywhere, even if the recipient can't do anything useful with them. The sync database holds all of the data, regardless of the client's ability to utilize it, and this means that you can regenerate from any device if something goes bump in the night.

You can currently embed an OmniGraffle file (and I presume an OmniGraphSketcher file, but don't have the iPad app to test this presumption) in an OmniFocus document on the Mac, and when it is synced to your iPad, it will show up as an attachment to the action or project where you put it. You can then open it in OmniGraffle (or OGS) though you have to be careful if you are going to make changes at the moment, you won't be able to send the changes back directly through OmniFocus. You also want to watch how many large files you attach or your database will get very large, leading to possible syncing slowdowns or even out-of-memory crashes.
I only have OF for iPad and iPhone. OO, OF, OG, OP for Mac. I don't store files in my databases for the reason you mentioned. I use sym links currently between my OG Mac apps. These would obviously not 'work' once synced to iPad or iPhone. They don't even show up in the notes field of OF iPad.

Thus my question...and I'm sure I wasn't clear. For the very reason you mentioned...bloat, crash, slow down issues...I don't want to store my iPad OG files IN the app. I'd like to see a 'parent' OG iPad app that houses the OG apps and their associated DB's that can link to the files rather than embed them. This group of DB's could be synched back to the desktop with a sync server like the one being used for OF. This way files from OG apps don't have to be stored IN the app...preventing the mentioned problems...and keeping desktop versions up to date.
Yeah, I understood what you were saying, and just wanted to expand a bit on what you could do right now. What's there now is useful, if restrictive.

I think the document interchange stuff in iOS right now (on the drawing board for OmniFocus, but not shipping yet in a general form) in conjunction with something like Dropbox might allow what you want without having to make the big "container app" you mention. I don't know how interested Omni is in hitching their wagon to someone else's horse, however. I'm also not sure how easy Apple has made it to get a reference to some other app's data; clearly there is a path to say "here's a file, please open it" but I don't know if there's a means to say "give me a handle to this file I'm giving you that I can give back to you in the future and have you open it"...
Sadly, file management is one way. I hope that Apple changes that in the future. Right now there is no good way to sync data unless each app does their own sync. Having DropBox, MobileMe, or any other service let you open a document into iWork or any other app and save it back into the sync app: beautiful idea. I eagerly await it.
I agree file management restrictions by Apple make many features we take for granted in our desktop apps totally out of reach with iOS.

With regards to OG hitching their wagon to Dropbox or any other similar service, I think the Sync Server is the answer to that question. Being a user rather than a programmer, I can only voice what I'd like to see. I can't even imagine what it would take to code links...or if Apple would even allow it. Skyscape has a parent app that contains all of your purchased content. The UI isn't perfect, but it allows some linking between apps included in the main app. Not exactly what I'm hoping for from OG, but similar.

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