You'll need to do a full cluster restart from .90.x to 1.x (i.e. need to 
bring down all nodes). There is some information here to help reduce 
recovery/startup churn:

http://www.elasticsearch.org/webinars/elasticsearch-pre-flight-checklist/

But in general:

1) Stop all queries/indexing jobs

2) Flush your indexes: curl -XPOST "localhost:9200/_flush"

3) Shutdown your cluster: curl -XPOST "localhost:9200/_shutdown"

4) Backup all your data/ and config/ folders (from all nodes if you have 
multiple data folders/nodes) - This is important in case the upgrade fails!
5) Per node, uninstall your current ES. Be careful not to delete the data 
folders and your config/ files

6) Per node, install new ES and pull in your config/* files from previous 
install

7) Verify all config files in all nodes and all data folders

8) Start all nodes one by one

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