Hi.
Have you given @hexparrot the archive he requested? He have after all narrowed this down to a bug he’s not been able to reproduce. Since you have a server with the bug active it may be of great help to him, and will most likely end up in a release where you can use the WebUI without it crashing.
@hexparrot discussed console commands for mineos here:
https://discourse.codeemo.com/t/mineos-console-js-documentation/998/3
As for running MineOS in shell only:
I would say that doing this you do not need the MineOS part installed at all, since the WebUI really just is a web based graphical layer for management.
to start a server it runs a command much like :
screen java -Xmx1024M -Xms1024M -jar minecraft_server.jar nogui
Just swap minecraft_server.jar with your jar file since you do not run a vanilla server.
To learn more about screen: https://www.mattcutts.com/blog/a-quick-tutorial-on-screen/
Archives are done by using the “tar” command: http://www.howtogeek.com/248780/how-to-compress-and-extract-files-using-the-tar-command-on-linux/
Backups are done with r-sync: http://everythinglinux.org/rsync/
The only thing left then is really the profiles, which really only provides handy buttons to download server-files to a local file reprository on your MineOS server. These can easily be downloaded manually, and just copied into the server directories you need them in.