gt shutdown was not stopping the daemon, which caused it to restart
agents (witnesses, refineries) after shutdown completed. The daemon
heartbeats every 3 minutes and calls ensureWitnessesRunning() and
ensureRefineriesRunning(), which would notice the sessions were dead
and restart them.
This adds daemon stop logic to both runGracefulShutdown (as Phase 6)
and runImmediateShutdown (after polecat cleanup), matching the behavior
that gt down already has.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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