First off, I should not give the wrong impression. Gratitude is due to 
Adam et. al. on this forum for a bibliography manager, and support 
community, that is by far best-in-class, and graciously offered for 
free.

Regarding the huge diffs, I am fully in agreement with Michael. Autofile 
is a great feature, and so is the preview side panel, and it would be a 
pity to view this as an either/or proposition. I just feel that the new 
BibDesk is somehow rubbing against the aesthetic and openness of the 
Bib(La)TeX format. Many if not all of us are scholars and share our 
materials with students and colleagues. Part of the appeal of this 
format is that its plain-text elegance and standardization liberate the 
data from any particular software. The very fact that BibDesk now 
presumes to "own" the database is a bit contrary to the philosophy of 
BibTeX, I think.

More practically, wouldn't this issue be solved if there was a scheme 
for storing the links locally in a separate file? I am thinking of a 
simple one-to-one index assigning each bibliographic entry (identified 
either by its BibTeX key or by a BibDesk-generate UUID) to a list of 
links to the entry's attachments?

For the time being, Michael, I am thinking to move my BibDesk-owned bib 
file out of the git repo and into dropbox, then use bibtool to produce a 
git-friendly version stripped of all links.

Thanks.

>> On Nov 12, 2015, at 9:32 AM, Maxwell, Adam R <adam.maxw...@pnnl.gov> 
>> wrote:
>> ...
>>> The autofilling of papers is fantastic, but the lack of portability, 
>>> and the noise in the diffs is really a huge wart for users like 
>>> macula and me.  I believe that a simple option in the preferences 
>>> for autofilling papers in a relocatable directory structure would 
>>> satisfy many users needs.
>>
>> Just use the Local-Url field, then, as Christiaan suggested. I think 
>> you lose autofill support
>
> ... Nooooo!  Autofile is a fabulous feature.  I still want Bibdesk to 
> autofile the papers, but after it autofiles them, I want it to fill in 
> the Local-Url field and then be done with it.  This is why I just live 
> with the noise so far.
>
>> and the file panes (and renaming/moving in Finder will break your 
>> links)
>
> I can live with that.
>
> Michael.
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