If you install or upgrade a theme within your WordPress Dashboard then you will see an AutoRestore|Quarantine message to click a link to complete AutoRestore backup – the entire process is automated and seamless. If you install Theme files remotely using a remote 3rd party plugin from a remote website you can exclude the /themes/ folder from being checked by ARQ so that Theme files do not get quarantined. If you are manually editing or uploading files via FTP then see these AutoRestore|Quarantine Manual File Editing/Uploading Correct Usage steps: http://forum.ait-pro.com/forums/topic/autorestore-quarantine-guide-read-me-first/#procedural-steps
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