WLSTException: MDS-01160: Expecting absolute document reference. Reference " /metadata/iam-features-OIMMigration/EventHandlers.xml" is a relative reference to the document.MDS-91009: Operation "exportMetadata" failure. Use dumpStack() to view the full stacktrace.
The reference in the error looked pretty absolute to me but upon further inspection of the metadata_files property there was a space after the comma. I removed all of the spaces from the line and re-ran weblogicExportMetadata.sh; and voila no more error.
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