Actually, it is related to the Jenkins working/home directory (see JENKINS-18459) as this is where Jenkins usually is given read/write access.

In an environment where Jenkins WAR is running inside an existing Tomcat application server with user 'tomcat7', Jenkins fails as the user does not have write access to the user's home directory (usually that's '/usr/share/tomcat7') for security reasons.

If the slave FS root solves this problem, that's perfect. Just make sure that the actual user running Jenkins has write access to this directory.

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