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/conftest.py

@@ -212,7 +212,7 @@ def asset_factory(http: requests.Session, api_base: str):
 
     for aid in created:
         with contextlib.suppress(Exception):
-            http.delete(f"{api_base}/api/assets/{aid}", timeout=30)
+            http.delete(f"{api_base}/api/assets/{aid}?delete_content=true", timeout=30)
 
 
 @pytest.fixture
@@ -258,4 +258,4 @@ def autoclean_unit_test_assets(http: requests.Session, api_base: str):
             break
         for aid in ids:
             with contextlib.suppress(Exception):
-                http.delete(f"{api_base}/api/assets/{aid}", timeout=30)
+                http.delete(f"{api_base}/api/assets/{aid}?delete_content=true", timeout=30)