It seems fair to say that Instapaper's version of an article can't be "redownloaded" for various reasons (offline, paywall, article removed, etc.) so it would be OK to put it in the Documents folder.
The argument against that is that you're now syncing that article with iCloud in addition to Instapaper.
But I wonder whether the correct answer is instead to eliminate Instapaper's sync feature, and just let iCloud do it. Once you have system-level cloud sync, don't you want to let Apple do the work? Sync is hard, and it isn't really the core value of Instapaper.
Edit: I was wondering about iCloud only for iOS 5/MacOS 10.7.2 devices with iCloud accounts. But that story does fall apart for people with mixed devices. So never mind.
I see it being a long while before everyone has iCloud up and running. We installed it last night on a relatively new MBP, to learn it doesn't work without Lion, so now we are upgrading to Lion. It will only work on certain phones, I believe 3GS and above.
Maybe Apple will release iCloud for Snow Leopard, but as it is now, instapaper works all the way down to the terrible version 2 iPhone I have had to resort to using in order to not sign into a new contract waiting on the release of the 4s.
Instapaper would hurt too many current users who are just fine with how things work without the cloud.
The argument against that is that you're now syncing that article with iCloud in addition to Instapaper.
But I wonder whether the correct answer is instead to eliminate Instapaper's sync feature, and just let iCloud do it. Once you have system-level cloud sync, don't you want to let Apple do the work? Sync is hard, and it isn't really the core value of Instapaper.
Edit: I was wondering about iCloud only for iOS 5/MacOS 10.7.2 devices with iCloud accounts. But that story does fall apart for people with mixed devices. So never mind.