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Use rel filepath in auto generated kustomization
This works around another bug on Windows platforms that would cause the kustomize-controller to choke on the kustomization.yaml generated by the bootstrap command due to the filepath being in a Windows format. By using `filepath.Rel`, the output is _just_ the filename for files relative to the bootstrap path, which is at the moment sufficient to make it work. Signed-off-by: Hidde Beydals <hello@hidde.co>pull/578/head
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