feat: soft-delete for AssetReference with scanner persistence

- Add deleted_at column to AssetReference model and migration
- soft_delete_reference_by_id sets deleted_at instead of removing rows
- DELETE /api/assets/{id} defaults to soft-delete; delete_content=true
  for hard-delete
- Add deleted_at IS NULL filters to read queries, tag queries, and
  scanner queries so soft-deleted refs are invisible
- restore_references_by_paths skips soft-deleted refs
- upsert_reference clears deleted_at on explicit re-ingest
- Add tests for soft-delete API behavior, scanner persistence, bulk
  insert, enrichment exclusion, and seed asset garbage collection

Amp-Thread-ID: https://ampcode.com/threads/T-019cb6fc-c05c-761f-b855-6d5d1c9defa2
Co-authored-by: Amp <amp@ampcode.com>

tests-unit/assets_test/services/test_asset_management.py

@@ -140,7 +140,7 @@ class TestUpdateAssetMetadata:
 
 
 class TestDeleteAssetReference:
-    def test_deletes_reference(self, mock_create_session, session: Session):
+    def test_soft_deletes_reference(self, mock_create_session, session: Session):
         asset = _make_asset(session)
         ref = _make_reference(session, asset)
         ref_id = ref.id
@@ -153,7 +153,11 @@ class TestDeleteAssetReference:
         )
 
         assert result is True
-        assert session.get(AssetReference, ref_id) is None
+        # Row still exists but is marked as soft-deleted
+        session.expire_all()
+        row = session.get(AssetReference, ref_id)
+        assert row is not None
+        assert row.deleted_at is not None
 
     def test_returns_false_for_nonexistent(self, mock_create_session):
         result = delete_asset_reference(