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I have written a wrapper for graffle-export that allows batch export of graffles to pdf or eps files on the command line.

The syntax is:

graffle.py <pdf|eps> input_dir/ output_dir/

If you already use graffle-export you can just grab the python script and put it
in the directory. The python script calls the shell script with the assumption that it is in the same directory.

https://github.com/jbremson/graffle-export