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It’s past 3 AM and I finally found out why after stopping my Tomcat server I’m unable to successfully start it again. It seem like Java process won’t go away. To get around that I added the following line to my Tomcat shutdown.sh script:
killall -9 java
and all is well now. Still unorthodox, but works for me. I will write a script to find the process and kill it properly later on.