[FEATURE] make --setup the default behavior and deprecate the flag #1211
Description
Currently several subcommands our CLI (update, server) accepts a --setup. Since --setup needs to be confirmed by users when there's any change needed, it's actually pretty safe if we always turn on --setup.
From now on, we want to always automatically execute setup-related logic for these subcommands, regardless of the --setup flag.
We still want to keep the --setup flag for a while for backward compatibility (users may have some script passing this flag in), but whenever users explicitly turned on --setup, output a warning to tell users it's deprecated.
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