I'm using BibDesk myself to organize my PDFs. It has built-in support  
for Skim notes, and accepts any sort of attached files (and in the  
near future multiple files per item). In fact, Skim was developed as  
a PDF viewer companion for BibDesk, so there's a good change for more  
and better integration in the future. Disclaimer: I am a developer of  
both programs.

Christiaan

On 7 Dec 2007, at 11:24 AM, Michael Garton wrote:

> Usage scenarios - how are you storing and organising your Skim files?
>
> I had been storing all my files in DevonThink Pro and have raised
> this issue on the forum there, but it seems there isn't a solution.
> DT will not import Skim notes or Skim pdf bundles files. I didn't
> intend to have Skim going head to head with DT, but that is my
> situation: I had to decide whether my marked up pdfs (and being able
> to amend and add to those notes i.e. Skim) were more important to me
> than the way they are archived (i.e. DT). Reluctantly, I am having to
> abandon DT.
>
> I suppose I am looking for a freeform database that will accept
> anything (not seek to scan content like DT does, which makes the
> software fussy about what file formats it can accept).
>
> So I have gone from being able to store, arrange and collate _all_ my
> pdfs but with restrictions on how I view/annotate them i.e. Preview
> and DT, to having a much more effective work environment for
> _individual_ files (Skim) but lost the ability to organise and
> retrieve the library.
>
> Help!
>
> Michael



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