What files get uploaded?
So here's the scoop: I formatted my hard drive recently without remembering to backup my Zotero standalone DB. Whoops! No problem, I thought - I'll re-install, and online DB will sync with my computer, and all will be well. This sort of happened. However, while the structure of the database is back (ie. every reference is where it should be), there seems to be no rhyme or reason as to which pdfs were saved on the online db, and which weren't. Does anyone know what's going on here? Also, is there a way that I can just have Zotero point to pdfs in my dropbox? That way I can mark them up on my ipad, for instance, and then have those markups exist in the Zotero versions of my pdfs. Thanks!
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Upgrade Storage
You can use links (right-click--> Add Attachment --> Add link to file) to any file on your harddisk, including of course in your dropbox folder. You can also use Zotfile to automatically move files to dropbox.
http://www.jlegewie.com/zotfile.html
If you do keep syncing through Zotero or through a WebDAV server, you can use one of the two available third party iOS apps to access Zotero data _and_ files on your ipad:
http://www.zotpad.com/
http://www.papershipapp.com/