QPDF is great! I use it heavily to analyze PDFs generated from other applications (PDFTeX, InDesign) to incorporate new features (such as spot colors) in my software (http://speedata.github.io/publisher/index.html) The command line I prefer is
However qpdf seems to have more features. The most interesting for me:
The QPDF library also makes it possible for you to create PDF files from scratch. In this mode, you are responsible for supplying all the contents of the file, while the QPDF library takes care off all the syntactical representation of the objects, creation of cross references tables and, if you use them, object streams, encryption, linearization, and other syntactic details.
A key part to take from the conversation:
"I also know from working with Tom Callaway that the theoretical solution of using the section 7 permission to remove additional restrictions is not one that Fedora generally wishes to use, perhaps as a matter of policy. I would add that, speaking for Red Hat as distributor, we do not wish to use that permission in this instance."
Ie: There is additional restrictions added to the AGPLv3 license in this specific case. The license allow fedora to remove them, but Fedora chooses not to do so.