Was requested to post a discussion topic to start rather than a github issue.
Original link: https://github.com/elastic/elasticsearch/issues/50323
The problem, as described in the issue, is that following the standard cluster upgrade guide from nodes on version 5.4 to 5.6, disk usage on each node doubled. This disk usage has not gone dropped even after the entire cluster finished the upgrade.
Some of the indices were originally created under version 5.3, some under version 5.4.
The question is: how can I force elasticsearch to clean up the disk usage? I assume there wasn't some atrocious change in the underlying data format that ballooned disk usage in version 5.6.
I also don't know very much about the ES data structure, so I don't know how to tell which shards are "leftovers".