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Simply manage your calibre library on your personal computer and use rsync to update the library on the server from your personal computer. The script that runs rsync should ssh into the server, stop the calibre-server process and then run rsync and then restart the calibre-server.
And it's on my TODO list to allow the calirbe GUI to conenct to a remote calibre-server instance as a device so you can manage the books on it comfortably.
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