there are log4j.properties in the jb files of the cobertura files.
If you are logging in with log4j, perhaps this file is used to register the configuration (log4j takes the first log4.properties from the class path and uses this).
you can delete this file from the lib library or make sure your logging configuration is the first in the classpath.
If you specify -Dlog4j.debug = true, then log4j will tell you which logging configuration file it uses.
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