fix(file-index): prune removed active assets on rebuild

Treat the source registry as authoritative during file-index rebuilds while preserving staged uploads. This prevents deleted archived sources from remaining searchable.

Tests: python3 -m unittest tests.test_file_assets tests.test_business_facts

tests/test_file_assets.py

@@ -55,6 +55,32 @@ class FileAssetIndexTests(unittest.TestCase):
         self.assertEqual(json.loads(rows[0]["pitch"]), ["0.5"])
         self.assertEqual(json.loads(rows[0]["pin_count"]), ["18"])
 
+    def test_rebuild_removes_active_records_removed_from_registry(self):
+        retained_id = "sha256:" + "c" * 64
+        removed_id = "sha256:" + "d" * 64
+        self._write_registry_record(
+            source_id=retained_id,
+            archive_path="_sources/archive/bjd/pdf/retained.pdf",
+            original_name="retained.pdf",
+            title="Retained source",
+        )
+        self._write_registry_record(
+            source_id=removed_id,
+            archive_path="_sources/archive/bjd/xlsx/removed.xlsx",
+            original_name="removed.xlsx",
+            title="Removed source",
+        )
+        rebuild_from_registry(self.vault, db_path=self.db_path)
+
+        retained_record = json.loads(self.registry_path.read_text(encoding="utf-8").splitlines()[0])
+        self.registry_path.write_text(json.dumps(retained_record) + "\n", encoding="utf-8")
+        rebuild_from_registry(self.vault, db_path=self.db_path)
+
+        remaining = search_assets(self.vault, "retained", db_path=self.db_path, limit=5, read_only=True)
+        removed = search_assets(self.vault, "removed", db_path=self.db_path, limit=5, read_only=True)
+        self.assertEqual([row["file_id"] for row in remaining], [retained_id])
+        self.assertEqual(removed, [])
+
     def _write_registry_record(self, **fields):
         record = {
             "record_type": "source_archive",