refactor(cli): rename plan lifecycle-list and lifecycle-apply to match specification

Renames `plan lifecycle-list` to `plan list` and `plan lifecycle-apply` to `plan apply` to align with the specification's canonical command names. Removes legacy V2 plan commands that occupied those names.

- Renamed CLI command registrations from lifecycle-list/lifecycle-apply to list/apply
- Removed legacy V2 apply and list commands (~200 lines)
- Updated apply shortcut in main.py to delegate to v3 lifecycle
- Added defensive null check for plan existence in apply command
- Updated 63+ test, doc, and benchmark files for consistency

Closes #881

Co-authored-by: Jeffrey Phillips Freeman <the@jeffreyfreeman.me>
Co-committed-by: Jeffrey Phillips Freeman <the@jeffreyfreeman.me>

robot/helper_m1_e2e_verification.py

@@ -298,9 +298,9 @@ def plan_full_lifecycle() -> None:
     """Run the plan lifecycle via real CLI subprocesses.
 
     Invokes action create -> plan use -> plan show -> plan execute ->
-    plan diff -> plan lifecycle-apply using the real ``agents`` CLI
+    plan diff -> plan apply using the real ``agents`` CLI
     binary.  Without an AI backend the plan stays in ``strategize /
-    queued``, so ``execute``, ``diff``, and ``lifecycle-apply``
+    queued``, so ``execute``, ``diff``, and ``apply``
     return graceful "not ready" messages rather than crashing.  The
     test verifies the full CLI wiring (DI, persistence, env vars)
     end-to-end.  ChangeSet verification uses the domain-level tests
@@ -390,8 +390,8 @@ def plan_full_lifecycle() -> None:
         if "INTERNAL" in combined5 and not is_expected_provider_unavailable(combined5):
             _fail(f"plan diff crashed:\n{combined5}")
 
-        # Step 6: Plan lifecycle-apply — similar: plan not ready
-        r6 = run_cli("plan", "lifecycle-apply", "--yes", plan_id, workspace=workspace)
+        # Step 6: Plan apply — similar: plan not ready
+        r6 = run_cli("plan", "apply", "--yes", plan_id, workspace=workspace)
         combined6 = r6.stdout + r6.stderr
         if "Traceback" in combined6:
             _fail(f"plan apply crashed:\n{combined6}")