fix(run): address gadfly review of the checkpoint PR

Real findings from the consensus review (44 raw; heavy devstral noise):

- finalizeCheckpoint is now fired from the top-of-Run defer, so it runs on
  EVERY exit: a panic, an early build-error return (before the run loop), AND
  normal completion. Previously an early return on a recovered run left its
  durable record unfinalized → boot recovery would retry it forever on a
  persistent build error. (opus + glm)
- Removed the dead ActivePhase field from run.RunCheckpointState +
  run.ResumeState (and the battery RunCheckpoint) — phase recovery is
  boundary-granular (skip completed phases; the interrupted phase re-runs from
  its start), so ActivePhase was never written nor read. Docs across
  ports/checkpoint/phases now state this plainly (5-model consensus that the
  field + docs over-promised mid-phase resume).
- CheckpointerFactory.Begin error is now logged (WARN) before degrading to
  non-durable, per the documented contract (was silently swallowed). (4 models)
- finalizeCheckpoint logs Complete/Fail errors (was silent).
- Resume phase-skip now keys off a SEPARATE resumeSkip set, not the live
  outputs map — a fresh run with two same-named phases no longer skips the
  second (the outputs map fills as phases run). (opus:max) + regression test.
- Removed the dead checkpoint.factory.now field (never set). (opus + glm)
- Fixed the stale phaseDeps doc (the step observer moved out of sharedOpts to
  per-path). Hoisted the resume guard to a local; dropped the wasted acc
  allocation on the resume path; documented that Save throttling is the
  Checkpointer's responsibility and the accumulated transcript is pre-compaction
  (host size-caps it).

Note (carried from the PR): classifyCheckpointOutcome keys shutdown on
run.ErrShutdown; mort stamps its own runengine.ErrShutdown — the mort wiring PR
aliases them so errors.Is matches.

New test: duplicate phase names both run on a fresh run. Full ./... green.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

run/phases_test.go

@@ -130,6 +130,26 @@ func TestPhases_OptionalDoesNotSwallowCancellation(t *testing.T) {
 	}
 }
 
+// TestPhases_DuplicateNamesBothRun: a fresh (non-resume) run with two phases
+// sharing a name must run BOTH — the resume-skip guard keys off a separate
+// resume set, not the live outputs map (which fills as phases run), so a phase
+// never skips a same-named sibling on a fresh run.
+func TestPhases_DuplicateNamesBothRun(t *testing.T) {
+	models, fp := phaseProvider(t, fake.Reply("first"), fake.Reply("second"))
+	ex := New(Config{Registry: tool.NewRegistry(), Models: models})
+	ra := RunnableAgent{
+		Name: "p", ModelTier: "test-model",
+		Phases: []Phase{{Name: "x", SystemPrompt: "P1"}, {Name: "x", SystemPrompt: "P2"}},
+	}
+	res := ex.Run(context.Background(), ra, tool.Invocation{RunID: "r"}, "Q")
+	if res.Err != nil {
+		t.Fatalf("run error: %v", res.Err)
+	}
+	if n := len(fp.Calls()); n != 2 {
+		t.Fatalf("both same-named phases must run on a fresh run; got %d model calls", n)
+	}
+}
+
 // TestPhases_HardErrorAborts: a NON-optional phase that hits a hard error (not a
 // budget/step exhaustion) aborts the pipeline; later phases do not run.
 func TestPhases_HardErrorAborts(t *testing.T) {