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there is no error re-applying a config at the start of every jenkins - unless you are starting jenkins manually (in which case you shouldn't need to do that).
You can set it in the init script or sysconfig/jenkins on unixy machines and the jenkins.xml on windows
unix
JAVA_ARGS="-Dhudson.model.WorkspaceCleanupThread.disabled=true ...some_other_args"
windows
<arguments>-Xrs -Xmx256m -Dhudson.model.WorkspaceCleanupThread.disabled=true
-Dhudson.lifecycle=hudson.lifecycle.WindowsServiceLifecycle
-jar "%BASE%\jenkins.war" --httpPort=8080</arguments>
Give there is a simple way to set this (and it is not something that should be set in normal use cases) I would recommend closing this issue.