I want to know if it is possible for elasticsearch to index documents into 2 directories. One for me to use, and then another as a backup. I want to create a mirror of all the indices as a backup.
It depends on exactly you mean by backup. 
If you have multiple ES servers then the default configuration has a replica for each shard. This protects you against a single machine failure -- the replica shard is promoted and continues providing service, and if another server is available a new replica is spun up on it.
If you are running on a single server and want to backup and restore data then snapshot might be what you are looking for.
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