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>

app/assets/services/asset_management.py

@@ -10,6 +10,7 @@ from app.assets.database.queries import (
     reference_exists_for_asset_id,
     delete_reference_by_id,
     fetch_reference_and_asset,
+    soft_delete_reference_by_id,
     fetch_reference_asset_and_tags,
     get_asset_by_hash as queries_get_asset_by_hash,
     get_reference_by_id,
@@ -130,6 +131,14 @@ def delete_asset_reference(
     delete_content_if_orphan: bool = True,
 ) -> bool:
     with create_session() as session:
+        if not delete_content_if_orphan:
+            # Soft delete: mark the reference as deleted but keep everything
+            deleted = soft_delete_reference_by_id(
+                session, reference_id=reference_id, owner_id=owner_id
+            )
+            session.commit()
+            return deleted
+
         ref_row = get_reference_by_id(session, reference_id=reference_id)
         asset_id = ref_row.asset_id if ref_row else None
         file_path = ref_row.file_path if ref_row else None
@@ -141,7 +150,7 @@ def delete_asset_reference(
             session.commit()
             return False
 
-        if not delete_content_if_orphan or not asset_id:
+        if not asset_id:
             session.commit()
             return True