How do you organise scientific articles with and without annotations? Like most of you, I read several scientific articles every week and annotate them on my tablet. 

Do you know of a useful way to organise "clean" vs "annotated" articles in a way that is searchable and mobile-device friendly? 

I use Papers now, but it isn't useful to have two copies of everything: a clean one and an annotated one. 

Maybe one of you guys have a brilliant method to deal with this.
Mendeley


This should cover nearly all your requirements -- with or without annotation.

Although my personal choice would be BibDesk (which I use nearly every day), Mendeley hits it for a cross-platform mobile-friendly experience.