To run single-file conversions from the keyboard, you can use the
pdf-to-pdf_embed script in 'humanengr's Skim scripts' on
http://sourceforge.net/p/skim-app/wiki/AppleScript/#user-contributed-scripts.
The script contains the set-up instructions for the keyboard shortcut.

On May 8, 2015, at 10:41 AM, Jan Jakob Bornheim
<jjbornh...@gmail.com> wrote:

>
> On Fri, May 8, 2015 at 7:32 PM, Rob MacLeod
> <macl...@cvrti.utah.edu> wrote:
>> Hi
>>
>> Thanks guys for the rapid and licid response. I will continue to
>> experiment to find a workflow that allows me to take advantage of the
>> benefits without the mishaps.
>>
>> Is there a quick, keyboard approach to exporting the pdf with markup?
>> I could probably even handle an AppleScript type solution and bulk
>> convert a whole directory full of marked up assignments for my
>> classes.
>>
>> Thanks, Rob
>
> The Skimalot (http://sourceforge.net/p/skim-app/wiki/Shell_Scripts/)
> shell script can handle batch converting an entire folder, if you're
> comfortable using the terminal.
>
> Cheers,
>
> JJ
>
>>
>>
>> On May 8, 2015, at 9:12 AM, Jan Jakob Bornheim
>> <jjbornh...@gmail.com> wrote:
>>
>>> On Fri, May 8, 2015 at 5:03 PM, Christiaan Hofman
>>> <cmhof...@gmail.com> wrote:
>>>>
>>>> On May 8, 2015, at 15:12, Rob MacLeod wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I have used Skim off and on for some years, just updated to the
>>>>> new version, and appreciate a great deal of what the program
>>>>> offers. I drift back to Preview at times but then get frustrated
>>>>> again with each new version and return to Skim for a while. This
>>>>> relationship is a little like serial monogamy and I am trying to
>>>>> figure out why I cannot commit to Skim as my lifelong partner (-:
>>>>>
>>>>> The main reason I leave Skim is the clumsy file management it
>>>>> requires and so I thought I would bring this up, perhaps as a
>>>>> topic long since discussed and put to bed. So please point me at
>>>>> the answers, if they exist somewhere on this list or the help
>>>>> pages.
>>>>>
>>>>> The clumsy part, of course, is the need to export the file each
>>>>> time I wish to save a version I can read with another pdf reader
>>>>> or send to another person. I use pdf markup for all my grading,
>>>>> much of the markup of papers and grants I collaborate on, and most
>>>>> anything else students or colleagues send to me for comment. So I
>>>>> guess I am a power user or at least a committed user of pdf markup
>>>>> tools. I have to share the results of those edits with others and
>>>>> most others do not use Skim--and I am not likely to change this
>>>>> behavior. As a result of need to share, I need to save
>>>>> conventional pdf files with the markup embedded and visible. Skim
>>>>> makes this harder to do that I would like and I wonder why the
>>>>> Skim designers figured their convention was useful. Why take a
>>>>> portable document format and make is non-portable?
>>>>>
>>>>> I try to be very careful about my workflow, saving the file each
>>>>> time through the export path, then ignoring the complaints from
>>>>> SKim when I close the file. But I have slipped up and I have lost
>>>>> edits and I have sent out strangely unmarked files to my students.
>>>>> I really should not have to worry about this. Why is the default
>>>>> not to save files with embedded markup? Can I change the default
>>>>> somehow to make it save standard pdf files?
>>>>>
>>>>> Thanks in advance for any guidance and counseling I might need to
>>>>> get over my hump with Skim and finally make it the tool I use all
>>>>> the time.
>>>>>
>>>>> Best
>>>>>
>>>>> Rob
>>>>>
>>>>>
>>>>>
>>>>> Rob MacLeod, PhD Professor of Bioengineering and Internal Medicine
>>>>> University of Utah Scientific Computing and Imaging (SCI)
>>>>> Institute Comprehensive Arrhythmia Research and MAnagement (CARMA)
>>>>> Cardiovascular Research and Training Institute (CVRT) 72 South
>>>>> Central Campus Drive Salt Lake City, Utah 84112 Email:
>>>>> macl...@sci.utah.edu URL: www.sci.utah.edu/~macleod
>>>>>
>>>>
>>>>
>>>> Yes, this has been discussed to death on this list before. Though I
>>>> don't have the links ready. There is also a discussion of it on the
>>>> Wiki. (And there is also no way this will change, so don't try.)
>>>>
>>>> The original reason for this is that when we started with Skim
>>>> PDFKit did not allow saving notes to the PDF. So partly this is
>>>> about backward compatibility. However this is by no means the only
>>>> reason. There are many reasons to have this. It has the notes as a
>>>> separate layer, so you also still have the original unedited PDF.
>>>> Also, you can view the notes separately. Most of all, PDFKit's
>>>> saving is too often really bad, it can lose you PDF data (partly
>>>> because PDFKit only supports older versions of PDF), or it can save
>>>> it inefficiently, and it often messes up the notes. Also, when it
>>>> is password protected, PDFKit can not simply save it, unlike Skim.
>>>> Moreover, saving and reason in Skim is because of this a lot
>>>> faster. And then there is backward compatibility with files saved
>>>> by Skim.
>>>>
>>>> Christiaan
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> Obviously, a number of good reasons. I just wanted to add that
>>> PDFKit really does save incredibly inefficiently. I have a number of
>>> scans from old books downloaded from archive.org[1]. The PDFs are
>>> usually around 30 Mbytes. Saving them with embedded notes or in
>>> Preview will bloat it up to beyond 300 Mbytes, saving notes the Skim
>>> way leaves the size virtually unchanged. On a smaller scale, a
>>> similar effect can be seen with any scanned PDF. Also, PDFKit has
>>> trouble handling a lot of non-English characters. Up until Mac OS X
>>> 10.11, saving a PDF with certain fonts containing Umlauts or
>>> accented characters would always corrupt the entire PDF. Now with
>>> Yosemite, it only happens once every while, but it still incredibly
>>> frustrating. Once again, that does happen with the way Skim saves
>>> notes. For me, this was the feature that drew me to Skim in the
>>> first place.
>>>
>>> JJ
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Links:

  1. http://archive.org/
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