The stop_crowd.sh script does, when executed, not kill the the actual java process. It leaves it it some sort of zombie state - still active, but unresponsive.

It seems to be related to the catalina.pid not being set on startup.

If one however defines an environment variable CATALINA_PID=/opt/atlassian/crowd/latest/apache-tomcat/work/catalina.pid (or the location where tomcat expects the pid-file) the pid-file is created upon startup and stop_crowd.sh works as desired.

Resolution: CATALINA_PID should be set by default.