A workaround:

When you choose to autofile, BibDesk seems to move the PDF and the 
corresponding Skim file. So what you could do is temporarily change the folder 
files get filed to, autofile all publications in your database, and delete the 
remaining files in the old folder. Then change the autofile location back to 
the old setting and auto-file all publications once again to move them back. 
Might want to turn off the cloud syncing part while doing this.

Cheers

Jan Jakob

From:  Christiaan Hofman
Reply-To:  For general discussion about using BibDesk
Date:  Monday 16 March 2015 11:52
To:  For general discussion about using BibDesk
Subject:  Re: [Bibdesk-users] orphaned file search


On Mar 16, 2015, at 6:43, Jan David Hauck wrote:

Hello, 

I recently did an orphaned file search since my my mac had messed up some files 
and created duplicates of some of my pdfs after some home folder permissions 
issue related to a cloud storage folder.  I quickly wanted to find the 
duplicates but unfortunately Bibdesk didn't find only those but gave me an 
entire list of the hundreds of skim files that sit in the same folders (I 
automatically save those Skim note backups with the pdfs).  

So here my question:
Is there a way to have Bibdesk in the orphaned file search only show pdfs or, 
more specifically, an option to ignore skim-files as long as a pdf with the 
same name exists? 

Thanks,

Jan

No, there's no way to do this. 

Christiaan

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