It is more problematic than being deprecated, there is the following bug that 
prevents the use in some cases: Wheezy and Jessie.

https://bugs.launchpad.net/ubuntu/+source/pdfshuffler/+bug/656382

See comment: Andrew Lundin (galundin) wrote on 2014-03-23: qhich is fixed by 
using python-pypdf2

According to pdfshuffler upstream, pdfshuffler works with python-pypdf2: 
http://sourceforge.net/p/pdfshuffler/bugs/19/

Thank you

greg


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