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>

alembic_db/versions/0002_merge_to_asset_references.py

@@ -79,6 +79,7 @@ def upgrade() -> None:
         sa.Column("created_at", sa.DateTime(timezone=False), nullable=False),
         sa.Column("updated_at", sa.DateTime(timezone=False), nullable=False),
         sa.Column("last_access_time", sa.DateTime(timezone=False), nullable=False),
+        sa.Column("deleted_at", sa.DateTime(timezone=False), nullable=True),
         sa.CheckConstraint(
             "(mtime_ns IS NULL) OR (mtime_ns >= 0)", name="ck_ar_mtime_nonneg"
         ),
@@ -104,6 +105,7 @@ def upgrade() -> None:
     op.create_index(
         "ix_asset_references_owner_name", "asset_references", ["owner_id", "name"]
     )
+    op.create_index("ix_asset_references_deleted_at", "asset_references", ["deleted_at"])
 
     # Create asset_reference_tags table
     op.create_table(
@@ -188,6 +190,7 @@ def downgrade() -> None:
     op.drop_index("ix_asset_reference_tags_tag_name", table_name="asset_reference_tags")
     op.drop_table("asset_reference_tags")
 
+    op.drop_index("ix_asset_references_deleted_at", table_name="asset_references")
     op.drop_index("ix_asset_references_owner_name", table_name="asset_references")
     op.drop_index("ix_asset_references_last_access_time", table_name="asset_references")
     op.drop_index("ix_asset_references_created_at", table_name="asset_references")