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You read papers, right? How do you store and organize them? I’m looking for advice on a workflow for annotating PDFs and syncing between devices.

I’m striking out on iPad apps for organizing scholarly papers. Papers2 doesn’t pull annotated copies back. Mendeley lite doesn’t even let me log in ((In Mendeley v1.3.1 (build 19) when I enter my login details, the only option is ‘close’. After closing, Mendeley reports “Not logged in”. Yes, I’ve double-checked my password!)). Zotero, which has been my main reference manager for at least 5 years, doesn’t offer an iPad app.

For annotation, I like iAnnotatePDF and GoodReader (and I’m getting ready to try PDFExpert). What I don’t know is how to have manageable filenames, when the documents originate in another iPad app, instead of on the desktop.

The only ideas I have left involve either spending more time with filemanagers or relying on the synching inside the annotation tools.

Reference managers/PDF managers:

1. Try Sente
2. See what DevonThink Pro Office can do, maybe with Zotero export others have worked on. Surely that’s overkill?

Synching from annotation tools:

iAnnotate or GoodReader can “watch” folders. Main challenge is going to be coming up with a sufficiently small collection of PDFs to sync back and forth to the iPad.

1. Stick with Zotero, maybe with files renamed from Zotfile, then use iAnnotatePDF’s “watch folder” feature to keep in sync.
2. Stick with Papers2, manually manage the file synch for everything I’ve annotated, then use watch its data directory with iAnnotatePDF as above.
3. Try Mendeley, watch its data directory with iAnnotatePDF as above.

Thoughts and suggestions? What would you do?