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Really sorry, I accidentally started running it without the dry run option. So it did it for real for some of the rows.
It completed aawiki, cawiki, commonswiki, deploymentwiki (this does not have Flow), dewiki, en_rtlwiki, and started enwiki.
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Done:
foreachwiki extensions/Flow/maintenance/FlowExternalStoreMoveCluster.php --from=cluster1 --to=flow_cluster1|tee /home/mattflaschen/external_store_real_run_all_wikis_2016-06-16.txt