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This can be done as a parameter to the "java" binary when starting Jenkins:
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java -Dhudson.util.ProcessTree.disable=true -jar jenkins.war
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A convenient way to achieve that is to change the environment variable BUILD_ID which Jenkins's ProcessTreeKiller is looking for. This will cause Jenkins to assume that your daemon is not spawned by the Jenkins build. For example:
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BUILD_ID=dontKillMe /usr/apache/bin/httpd
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| Info |
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In case of Jenkins Pipeline use |