There is some trouble with the moderation system, so I'll answer
directly to your next question:
As in our software we already refer to the latest version of Commons
IO, is it possible to also have a distribution without Commons IO
inside the jar?
No, because you don't need pdfbox-app unless for stand-alone use. Use
"pdfbox" without the "-app" like this (if you use maven) and then you
can use a different version of commons-io:
<dependency>
<groupId>org.apache.pdfbox</groupId>
<artifactId>pdfbox</artifactId>
<version>....</version>
</dependency>
Tilman
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