Separate RC10 manifest provenance warnings

scripts/audit_data_operations.py

@@ -426,7 +426,9 @@ def build_report(
         raise RuntimeError(f"Storage root is not a directory: {root}")
     records, skipped_symlinks = inventory_storage(root)
     database = collect_database_state(db, root)
-    references: set[Path] = expand_manifest_references(database.pop("references"), root)
+    direct_references: set[Path] = database.pop("references")
+    references = expand_manifest_references(direct_references, root)
+    manifest_references = references - direct_references
     cutoff = utc_now() - timedelta(days=minimum_age_days)
 
     categories: dict[str, dict[str, Any]] = defaultdict(
@@ -440,9 +442,14 @@ def build_report(
         item["cleanup_eligible"] = item["cleanup_eligible"] or record.cleanup_eligible
 
     existing_paths = {record.path for record in records}
-    missing_references = sorted(
+    missing_direct_references = sorted(
         path.relative_to(root).as_posix()
-        for path in references
+        for path in direct_references
+        if path not in existing_paths and not path.is_dir()
+    )
+    missing_manifest_references = sorted(
+        path.relative_to(root).as_posix()
+        for path in manifest_references
         if path not in existing_paths and not path.is_dir()
     )
     referenced_directories = tuple(path for path in references if path.is_dir())
@@ -479,8 +486,12 @@ def build_report(
         "database": database,
         "integrity": {
             "referenced_path_count": len(references),
-            "missing_referenced_path_count": len(missing_references),
-            "missing_referenced_paths": missing_references[:max_candidate_records],
+            "direct_database_reference_count": len(direct_references),
+            "missing_referenced_path_count": len(missing_direct_references),
+            "missing_referenced_paths": missing_direct_references[:max_candidate_records],
+            "manifest_artifact_reference_count": len(manifest_references),
+            "missing_manifest_artifact_count": len(missing_manifest_references),
+            "missing_manifest_artifacts": missing_manifest_references[:max_candidate_records],
             "skipped_symlinks": skipped_symlinks[:max_candidate_records],
         },
         "cleanup": {
@@ -507,6 +518,7 @@ def build_report(
         "limitations": [
             "The audit never downloads or refreshes an official source.",
             "Failed jobs and analysis runs remain provenance and are reported, not deleted.",
+            "Missing non-authoritative manifest intermediates are reported separately from direct database artifacts.",
             "Unknown storage categories are protected by default.",
             "No cleanup is scheduled implicitly.",
         ],

scripts/run_rc10_data_operations_audit.sh

@@ -88,6 +88,9 @@ manifest = {
         family: len(items) for family, items in families.items()
     },
     "missing_referenced_path_count": 0,
+    "missing_manifest_artifact_count": audit.get("integrity", {}).get(
+        "missing_manifest_artifact_count", 0
+    ),
 }
 (root / "manifest.json").write_text(
     json.dumps(manifest, indent=2, sort_keys=True) + "\n",