ISPconfig 3 does not have to possibility to upload .pkg files from ispconfig 2. The ispconfig 2 software repository system is completely different and there is no documentation available about it yet.
I looked now a little bit in the repository package system of ISPConfig 3 and I also made my own server for testing. The question is if the system is already for use, because the $conf["software_updates_enabled"] is false on standard.
