Great! It probably almost works.
1 - indeed, start with syncing your calibre database. Then check again. and post again if there are problems or questions. Or if it works!
2 - problems with /home (and /home/pirate/books/data/library/ is a part of /home) are limited (as far as I know) to Synology.
3 - as far as I know there is no such thing as you wish for. There are to many possible choices to properly maintain such a tool and keep it working with every new update of packages.
4 - don't see the command line as something evil, but as an opportunity to learn! ;-)
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