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Pyarlo has been installed on Johnny's python 3.6 https://krydos2.heliohost.org/cgi-bin/modules36.py It might be possible to import it from a folder on your account, but I've never put any effort into figuring out how to do that because it's easier to just install it.
Tomcat probably needs to be restarted before the logs will be recreated. The way I clear logs like catalina.out is cat /dev/null > /opt/tomcat/live/logs/catalina.out
The daily type logs it's probably fine to outright delete the old ones. To shutdown tomcat run
/opt/tomcat/live/bin/shutdown.sh
and then to start it again run
/opt/tomcat/live/bin/startup.sh
I had a guy on discord report that the multiphp button would just load a blank page. The solution for him was to disable his adblocker, and then it started working just fine.
There is an x3 imitation theme called paper_lantern retro that looks the same as x3 used to, but is actually paper_lantern still.
On Facebook you said you were using python 3.6 (/usr/bin/python3.6), and now you say you're using the default which is python 2.7 (/usr/bin/python). Can you verify which shebang you're using?
You were actually suspended because of /home/lsuarts/public_html/beta/wp-content/plugins/vwcleanerplugin/
That plugin was actually a backdoor and hackers were using your account to send spam.
Does the connection break if you connect directly to the .war via port 8080 rather than using the proxy through apache. That should narrow it down to whether apache or tomcat is the issue.