A late addition to this discussion, as I found out the best way to do this with 
some newer functions of the default command.

The way to backup and restore preferences nowadays is to use the defaults 
command in particular the export and import options. This works in one step, no 
need to delete files and whatever. Basically, you should never touch or use the 
the files in ~/Library/Preferences, as their function is completely opaque and 
mostly unpredictable, they may or may be related to the actual preferences that 
are used.

Basically, when you want to backup the bookmarks use:

        defaults export net.sourceforge.skim-app.skim.bookmarks 
path/to/some/backupFile.plist

And when you want to later restore the backup, use “import” instead of 
“export”. That’s all that’s needed. For preferences this basically goes the 
same, just with a different domain (e.g. "-app Skim" instead of 
"net.sourceforge.skim-app.skim.bookmarks").

Christiaan

> On Apr 11, 2016, at 17:13, Stefano Deiuri <[email protected]> wrote:
> 
> Christiaan Hofman <cmhofman <at> gmail.com <http://gmail.com/>> writes:
> 
>> 
>> 
>> 
>> On Apr 11, 2016, at 13:45, Piet van Oostrum <piet-l <at>
> pietvanoostrum.com <http://pietvanoostrum.com/>> wrote:
>> Stefano Deiuri wrote:Piet van Oostrum <piet-l <at> pietvanoostrum.com 
>> <http://pietvanoostrum.com/>> writes:
>> 
>> I made a test. I uninstalled all Skim files with AppDelete, and
> Ireinstalled Skim. I did copy the file
> "net.sourceforge.skim-app.skim.bookmarks.plist" inLibrary/Preferences, and I
> use the command in Terminal "defaults read
> net.sourceforge.skim-app.skim.bookmarks" but my bookmarks didnot get back.
> Please helpThank youStefano
>> 
>> OK, I think it would work if you reboot your computer.But I have something
> else. A few years ago I was struggling with the same kind of stuff and I got
> the following advice that worked for me:1. In Terminal typedefaults delete
> net.sourceforge.skim-app.skim.bookmarksfollowed by ENTER.And then copy the
> "net.sourceforge.skim-app.skim.bookmarks.plist" to Library/Preferences"I
> think it is best to have Skim not running while you do this.-- Piet van
> Oostrum <piet <at> vanoostrum.org <http://vanoostrum.org/>>WWW: 
> http://pietvanoostrum.com/PGP <http://pietvanoostrum.com/PGP> key:
> [8DAE142BE17999C4]
>> 
>> 
>> 
>> So to summarize all the steps:
>> 
>> 0. Don’t run Skim
>> 
>> 1. Type in Terminal followed by Enter:
>> defaults delete net.sourceforge.skim-app.skim.bookmarks
>> 
>> 2. Copy the backed up file
> to net.sourceforge.skim-app.skim.bookmarks.plist in ~/Library/Preferences
>> 
>> 3. Type in Terminal followed by Enter:
>> defaults read net.sourceforge.skim-app.skim.bookmarks
>> 
>> 
>> 
>> Christiaan
>> 
> 
> After a few of attempts finally I made it. Thank you very much guys, I will
> make a donation for the quality of the App and support.
> 
> Stefano


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