If you want to open a program by clicking its file one has to edit/set the mime types. Do a right-click on the file and choose entry 'Set Run Action...' or something similar (I'm in a German desktop). A GUI comes up, just drag the program (executable) into that GUI or enter a command.and I haven't managed to get Calibre's reader to activate when an ePub file is clicked on
As far as I know you have to copy /root/Choices/MIME-types to /tmp//root/Choices/MIME-types at remastering - you can also put a 'cp' command into the remasterpup2 script to keep this automatically at next remasters. That's how the LazY Puppy LazY Remaster Suite is acting (lots of similar options can be set in a GUI before remastering).
Command:
cp -af /root/Choices/MIME-types /tmp/root/Choices/
Find the section work on /root in remasterpup2 and put it in!
Also there is a CBR-Pager on the forum.