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Plugin cli tools configures logging with whatever is in the logging.yml. If a file appender is configured for any of the logs this will cause creation of an empty log file. If a plugin was for example installed as root it will create empty logs at es.home/logs. This is problematic when for example plugins are installed as root and es is run as service. Logs will then be created in /usr/share/elasticsearch/logs and can later not be removed by for example dpkg -r or -purge. To avoid this, configure the logger to use an appender that writes to the same output that plugin cli tool does. This allows other components that are called from Plugin cli tool to write to the same terminal that plugin cli tool writes to by using the logging mechanism already in place. The logging conf is not read at all pb plugin cli tool. As a side effect, the loging level for components that are called from the plugin command such as the jar hell check can now be configured with -Des.logger.level which makes it easier to debug the jar hell check.