Fold the done plugin tuning back into config.fish and drop the conf.d
fragment: config.fish is read whole into interactiveShellInit, so Nix
assembles the interactive init at build time instead of fish autoloading
a separate conf.d file. functions/copy.fish stays a function file, the
idiomatic home for a lazily-autoloaded function.
Move the Module to modules/fish/fish.nix and mirror a real fish config
directory beside it: config.fish (interactive init), conf.d/done.fish
(the done plugin tuning, now a real conf.d file), and functions/copy.fish.
completions/ and themes/ are omitted as they have no content and git
cannot track empty directories.
