swarmctl setup with no subcommand checks the setup status first, then takes the open steps one at a time: prompts for input, shows a running action as one live line, prints the store keys, root token and new password under a warning until the operator confirms, and names the deploy option for a step this host cannot do. It calls the code of bao init, bao grant-bootstrap, user add, forge make-admin, agent create, agent permissions set and agent set-state. Refuses without root or a terminal.
init prints the store's keys and root token once and keeps none; with
--and-grant it goes on to the granter bootstrap in the same process.
grant-bootstrap does that step alone, reading the root token from a
hidden prompt or stdin. The token reaches bao only as BAO_TOKEN in the
child's environment.