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/database/queries/__init__.py

@@ -38,6 +38,7 @@ from app.assets.database.queries.asset_reference import (
     restore_references_by_paths,
     set_reference_metadata,
     set_reference_preview,
+    soft_delete_reference_by_id,
     update_reference_access_time,
     update_reference_name,
     update_reference_timestamps,
@@ -107,6 +108,7 @@ __all__ = [
     "restore_references_by_paths",
     "set_reference_metadata",
     "set_reference_preview",
+    "soft_delete_reference_by_id",
     "set_reference_tags",
     "update_asset_hash_and_mime",
     "update_reference_access_time",