After ive got through your readme, the answer was pretty obvious:
add a new system in /recalbox/share_init/system/.emulationstation/es_systems.cfg like this:
<system>
<fullname>Scripts</fullname>
<name>Scripts</name>
<path>/recalbox/share/roms/scripts</path>
<extension>.sh</extension>
<command>%ROM%</command>
<theme>Scripts</theme>
<platform>Scripts</platform>
<emulators/>
</system>
and put your .sh scripts in /recalbox/share/roms/scripts
for example wakeonlan.sh:
ether-wake -i wlan0 XX:XX:XX:XX:XX
ether-wake -i eth0 XX:XX:XX:XX:XX
works for me. Again thanks for your help