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A fork is fine. The branch simply referred to creating a branch in your own fork, which is optional, you can use the master branch if you like or create a dedicated branch, it makes no difference to me.
As for storing preferences, I suggest getting the code working with hard coded values in LibraryServer.__init__ first, once we have a better idea of how exactly it works we can worry about config for it.
Currently the server is designed for convenient use both from the GUI and from the command line. To maintain that with this functionality, you would probably need to pass a dict of username->(password, vl) to LibraryServer. When running from the GUI it can be stored as a JSONConfig object in calibre's usual preference hierarchy. When running from the command line, probably an option to read it from the specified file.
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