Does anybody know where the data of etherpad lite is stored? It is because I want to integrate it in my daily backup.
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Do you mean when Etherpad is installed on your server?
Looks like it is stored in 'dirty.db' - https://help.ubuntu.com/community/Etherpad-liteInstallation
You can either backup the database or there is a script at http://blog.codeborne.com/2011/10/etherpad-lite-migrate-data-from-dirtydb.html that migrates to SQL - perhaps you can modify it to dump to something else you can backup.