Aligned the archive stage with the new work directory layout

internal/app/runner_test.go

@@ -463,6 +463,9 @@ func TestExecuteStagesRunLocalArtifactsAndCanonicalPromotion(t *testing.T) {
 		if strings.Contains(out.LocalPath, string(filepath.Separator)+"runs"+string(filepath.Separator)) {
 			t.Fatalf("session manifest output should be canonical, got run-local path %q", out.LocalPath)
 		}
+		if out.ProducerRunID != summary.RunID {
+			t.Fatalf("producer_run_id = %q, want %q", out.ProducerRunID, summary.RunID)
+		}
 	}
 
 	runManifest, err := store.LoadRun(context.Background(), summary.RunManifestPath)
@@ -480,6 +483,47 @@ func TestExecuteStagesRunLocalArtifactsAndCanonicalPromotion(t *testing.T) {
 	}
 }
 
+func TestExecuteStagesSkippedStagePreservesExistingOutputsProvenance(t *testing.T) {
+	cfg := testConfig(t)
+	store := &manifest.LocalStore{}
+	manifestPath := manifestPathFor(cfg)
+
+	existing := manifest.New(cfg.Session.SessionID, time.Date(2026, 5, 3, 1, 0, 0, 0, time.UTC))
+	existing.MarkStageSucceeded("transcribe", time.Date(2026, 5, 3, 1, 1, 0, 0, time.UTC), []manifest.ArtifactRecord{
+		{
+			Kind:          "transcript_raw",
+			LocalPath:     "transcripts/raw/alice.json",
+			ProducerRunID: "20260501T000000Z-deadbeef",
+		},
+	})
+	if err := os.MkdirAll(filepath.Dir(manifestPath), 0o755); err != nil {
+		t.Fatalf("MkdirAll() error = %v", err)
+	}
+	if err := store.Save(context.Background(), manifestPath, existing); err != nil {
+		t.Fatalf("Save manifest error = %v", err)
+	}
+
+	summary, err := executeStages(context.Background(), cfg, []stage.Stage{BuildFullPlan()[1]}, RunOptions{})
+	if err != nil {
+		t.Fatalf("executeStages() error = %v", err)
+	}
+	if len(summary.Skipped) != 1 || summary.Skipped[0] != "transcribe" {
+		t.Fatalf("summary = %#v, want skipped transcribe", summary)
+	}
+
+	loaded, err := store.Load(context.Background(), manifestPath)
+	if err != nil {
+		t.Fatalf("Load manifest error = %v", err)
+	}
+	got := loaded.Stages["transcribe"]
+	if got == nil || len(got.Outputs) != 1 {
+		t.Fatalf("transcribe outputs = %#v, want one preserved output", got)
+	}
+	if got.Outputs[0].ProducerRunID != "20260501T000000Z-deadbeef" {
+		t.Fatalf("producer_run_id = %q, want preserved value", got.Outputs[0].ProducerRunID)
+	}
+}
+
 func TestAdapterBackedStageFailureMarksManifestFailed(t *testing.T) {
 	cases := []struct {
 		name string