agentctl stop <id> fails with 'Session not found' while list/status show same id as running (desync)

[doink-kindo]

Repro

$ agentctl list -a | grep af7d0a1a
af7d0a1a  running  opencode     ohm/moonshotai/Kimi-K2.6  ~/code/mono-auto-ENG-10311  52894  1m ago  ...

$ agentctl status af7d0a1a
ID         af7d0a1a
Status     running
...

$ agentctl stop af7d0a1a
Session not found: af7d0a1a-4933-4441-8f80-9180d198caf4

$ agentctl stop af7d0a1a --force
Session not found: af7d0a1a-4933-4441-8f80-9180d198caf4

$ agentctl stop af7d0a1a-4933-4441-8f80-9180d198caf4 --force
Session not found: af7d0a1a-4933-4441-8f80-9180d198caf4

Expected

stop should terminate any session that list -a and status agree is running.

Actual

stop reports 'Session not found' even though list and status (with the same short id) successfully resolve and report the session as running. Looks like a daemon/session-state mismatch where list and status read filesystem session metadata but stop queries a different (daemon) registry that lost the entry.

Impact

Blocks SOP-driven cleanup (in this case the Linear ticket-undelegation SOP). Forced fall-back to identifying the wrapper PID from list output and kill -TERM on the wrapper + child opencode process, plus manual worktree teardown. Doable but error-prone for newer agents.

Context

• agentctl version: $(agentctl --version) — current
• Adapter: opencode running ohm/moonshotai/Kimi-K2.6
• Wrapper script: ~/.agentctl/opencode-sessions/wrapper-af7d0a1a-4933-4441-8f80-9180d198caf4.sh
• Session was launched ~1 min before the stop attempt
• Same shell, same uid

Suggested

1. Have stop consult the same source of truth as list/status.
2. If the daemon registry is missing the session, fall back to filesystem-derived PID and SIGTERM/SIGKILL the wrapper + child process group.
3. Surface a clearer error like "daemon registry desynced from session metadata — try agentctl prune then re-list" so the operator knows the right workaround.

Filed per AGENTS.md policy (file first, work around second). Encountered during the ENG-10311 undelegation SOP — worktree + branches were preserved; PR #11018 left open.