Currently, most of the logging is done straight to standard-out or standard-error. Instead, a logging framework should be used.
To combine all logging frameworks that might ship with dependencies, we should add SLF4j, and introduce corresponding bridges.
SLF4J, backed by Logback, has been introduced. There's a logback.xml config file that's part of the website that can be used to configure logging. For now, I left everything as a console-logger (which makes statements end up in catalina.out on Tomcat).
All output to std-out and std-err that I could find have been replaced by a Logger instance.