I use Dropbox's syncing softwave and have this same problem. I use the 
following technique, which helps somewhat, but it's not 100% safe.

In general preferences, turn on "Automatically save Skim notes backups" (on all 
machines where you use Skim).

Now when you save foo.pdf at the office, you'll also write to a normal file 
foo.skim, which contains the notes in addition to the file's xattrs. So this 
file will sync normally with whatever syncing software you use. And when you 
open foo.pdf from home, Skim will say: no notes found, but backup file found; 
do you want to load those?

The danger is, depending on how your syncing software works, you can end up 
with multiple note sets for a pdf, and end up overwriting newer data with 
older. Suppose you open foo.pdf from home, and it prompts you to load in the 
foo.skim backup file. Great. Now you add more notes, and save. Great again, all 
of your notes get saved to the xattrs as well as the backup file. But now you 
go back to the office, where the local file system already has xattrs notes for 
foo.pdf--the OLD xattrs. It's my understanding that in this case, Skim won't 
prompt you to load the backup notes file, even those it's newer than the xattrs 
and contains more data. It won't even warn you there's conflicting data. Worse, 
now if you make a change to foo.pdf at the office, when you save it again, 
you'll overwrite the backup file with the data from home.

Current versions of Dropbox SEEM to re-download foo.pdf after it's been saved 
by Skim from another location, thereby wiping out the local xattrs, even though 
no relevant data in the file has changed. Because of this inexplicable 
behavior, I haven't lost data in a while. But I'm on thin ice, I'm sure.

So basically, there is no good way to use Skim in these situations. Moreover, 
the developer is not interested in making the "backup" files anything more than 
backups, despite the use people are already forced into putting them to.

I don't think there is even a way to save as a "PDF bundle" by default. That 
would break easy compatibility with other PDF apps, but at least it would work 
reliably with most syncing software.

Good luck,
Jeremy


On Jun 7, 2010, at 6:33 PM, Brennon Bortz wrote:

> Does anyone use store files they edit with Skim in Git repositories?  My 
> heart was broken today to come home and find that all the work I'd done in 
> Skim the office didn't make the trip to the repository along with the .pdfs 
> themselves once Git was done with them.  Git doesn't xattrs--in fact, it 
> wipes them.  In fact, lots of file syncing and VCS utilities do this.
> 
> This is no problem for certain uses of extended attributes.  Frankly, there 
> are certain things that OS X uses xattrs for that I wouldn't want travelling 
> around in shared repos.  However, xattrs are meant for, well, attributes--not 
> file data (or, "data I want to associate with another file's data").  I 
> understand that this is a necessary hack for Skim's purposes (and an elegant 
> one, no less), but frankly somewhat antithetical to the purpose of 
> attributes.  So has anyone figured out a way to pass around Skim-edited files 
> in VCS systems, etc. and keep those precious notes?  Here's to hoping so!  
> <Lifts whiskey...>
> 
> Thanks,
> 
> Brennon Bortz
> Software Researcher
> Dundalk Institute of Technology
> [email protected]
> Ph.D. Researcher & Composer - Sonic Arts Research Centre
> Queen's University, Belfast
> [email protected] / [email protected]
> 
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