[bhaak]

Originally Posted by Aeris

I'd prefer to keep Kindle Menu only for exetensions stuff (not things that are installable through .bin), and to keep only one shortcut for the best app for each task... [...]

This is the first rule of software development: There are always users that have a different idea on what they want to do with your software than you do.

As you are starting KOreader with a shell script, you could check if KOreader exists, if it does start it else check if HackedUpReader exists and start it.

#!/bin/sh

if [ -f /mnt/us/koreader/koreader.sh ]; then
  sleep 12
  /mnt/us/koreader/koreader.sh /mnt/us/documents
  # wait the script to finish, i.e. until koreader closes
  wait
  # sleep a while until chrome bar is displayed again
  sleep 4
  /mnt/us/extensions/kindlemenu/bin/sh/batterylevel.sh
  /mnt/us/extensions/kindlemenu/bin/shortcut.sh
elif [ -f /mnt/us/hackedupreader/bin/cr3 ]; then
  /mnt/us/hackedupreader/bin/cr3
fi

I hope that works within Kindle Menu, I only tested the shell script.