Rework CLI command surface: hybrid grouping + deprecated aliases

[jrob5756]

Summary

Rework the top-level CLI command surface so commands are grouped more
logically. Keep the hot-path verbs flat, move the long tail under noun groups
(alongside the existing registry group), add cosmetic --help panels, and
provide backward-compatible deprecated aliases so existing invocations keep
working.

Current state

Top-level is a flat list that mixes hot-path verbs with rare admin/lifecycle
commands, all in one undifferentiated --help block:

run, validate, show, resume, checkpoints, replay, stop,
gate-respond, update + the registry group.

Proposal (Option C — hybrid)

Flat (unchanged invocation): run, resume, validate, show, stop,
replay, update

Noun groups:

• registry → list / add / remove / set-default / update / show
  (existing)
• gate → respond (+ room for future gate list) — new group
• checkpoint → list (+ room for future clean / show) — new group

Deprecated aliases (kept working, print a one-line stderr deprecation
warning, forward to the shared implementation):

• gate-respond → gate respond
• checkpoints → checkpoint list

Help panels via Typer's rich_help_panel= (supported in 0.21):

• Author & Inspect: validate, show
• Run & Recover: run, resume, stop, replay
• Interact: gate
• State: checkpoint
• Environment: registry, update

Backward compatibility

• No breaking change on merge — checkpoints and gate-respond remain valid,
  emitting a deprecation notice and forwarding to the new commands.
• Soft removal target: next major.
• replay stays flat for now (could later fold into a log/debug group).

Implementation sketch

1. Extract the checkpoints (cli/app.py:997) and gate-respond
   (cli/app.py:1274) command bodies into importable shared functions — no
   behavior change.
2. Add cli/checkpoint.py (checkpoint_app) and cli/gate.py (gate_app)
   modeled on cli/registry.py; register via app.add_typer(...).
3. Keep the old commands registered as thin deprecated aliases that warn +
   forward to the shared functions.
4. Add rich_help_panel= to top-level commands and groups.

Tests

• New group commands checkpoint list / gate respond.
• Alias deprecation warning is emitted and output matches the new command
  (forwarding parity).
• Audit existing checkpoints / gate-respond tests — repoint to new paths or
  keep as alias coverage.

Docs

• docs/cli-reference.md — retitle checkpoints→checkpoint list,
  gate-respond→gate respond; document the aliases.
• AGENTS.md — update the cli/ bullet list + "Common Commands".
• CHANGELOG.md — Deprecated (aliases) + Added (groups).

[jrob5756]

Starting to take a look at this.