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Simply write a script that stops the server and then launches calibre and starts the server when calibre quits. You can also have the GUI run its embedded server automatically on startup so your server downtime is not going to be down for more than a few seconds. It's only linux that has this pretty artificial distinction between servers that can have no GUI and GUI programs that cannot run 24x7.
The GUI is never going to be able to connect to a server as a backend, but the server is going to gain the ability to edit metadata/add/convert books, etc. via its own UI.
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