This is indeed not possible. Using a relative/absolute papers folder  
is an app setting, and cannot be done per document. You can use  
different sub-folders for different files using a key in the file  
info for the documents, and including a %i specifier in the local  
file format. You have to make sure though that all bibtex files have  
this key set before any autofile is done.

Christiaan

On 12 Jun 2007, at 4:41 AM, Kasper Daniel Hansen wrote:

> Hi
>
> I have for a long time now used the autofile feature of Bibdesk with
> great success. For various reasons I want to split up my papers
> folder into two different folders, each set of folders will have
> their own Library. I would now want to store my pdf files like
>    project1.bib -> project1folder
>    project2.bib -> project2folder
> These two folders will reside in completely different locations. I
> would also like to use relative paths for _one_ of the two projects.
>
> Is there any way to set preferences in Bibtex based on the bibtex
> file being modified? (I suspect not)
>
> I _might_ be able to think up a hack using custom fields in the
> bibtex file, but that will most likely be quite nasty.
>
> (One of the reasons for doing this is to put a set of papers into a
> subversion repository as part of a bigger (private) project. I would
> like the local-url argument to be handled with grace when several
> collaborators have their own file setup).
>
> Kasper



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