When Jenkins is using a buildsDir that is outside $JENKINS_HOME/jobs the archive contains relativized path ../.

For example JENKINS_HOME=/tmp/jenkins_home and using the system properties -Djenkins.model.Jenkins.buildsDir=/tmp/jenkins_home/builds/${ITEM_FULL_NAME}, getting a build bundle of build myfolder/myjob #13 would result in files like the following:

items/../builds/myfolder/myjob/13/build.xml
items/../builds/myfolder/myjob/13/changelog12345678901234467.xml
items/../builds/myfolder/myjob/13/log
items/../builds/myfolder/myjob/13/log-metadata
items/../builds/myfolder/myjob/13/workflow/flowNodeStore.xml