stop fails with 'Session not found' for a session that list/status report as running

[c-h-]

Summary

agentctl stop <short-id> fails with Session not found for a running session that agentctl list -a and agentctl status <short-id> both successfully resolve and report as running with a live PID. This forces a manual kill of the underlying process to actually stop the work — a ghost-session inconsistency between the read path and the stop path.

Repro (observed)

Session short id: 5b0abf14 (claude-code, model claude-fable-5), running QA in a worktree.

$ agentctl list -a
5b0abf14  running  claude-code  claude-fable-5  ~/code/mono-auto-ENG-10853  53208  11m ago  EXECUTE THIS PROCEDURE...

$ agentctl status 5b0abf14
ID         5b0abf14
Status     running
PID        53208
...

$ agentctl stop 5b0abf14
Session not found: 5b0abf14-3cf5-4eef-949a-741ca0001e1e

$ agentctl status 5b0abf14
Status     running          # still running; process 53208 alive

The process was still alive after stop; only a direct kill -TERM/-KILL 53208 (plus killing the child PID) actually stopped it.

Expected

stop <short-id> should resolve and terminate the same session that list/status resolve from the same short id. If the id resolves for the read commands, it must resolve for stop.

Notes

• The stop path expands the short id to 5b0abf14-3cf5-4eef-949a-741ca0001e1e and then reports it as not found, while the read path (list/status) resolves the short id fine — suggests a lookup/registry mismatch between the read and mutation code paths (or a stale/duplicate session record).
• Workaround: manual kill of the PID from agentctl status, then kill child PIDs (pkill -P <pid>).
• Environment: macOS (Darwin arm64), agentctl launching claude-code.