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/models.py

@@ -105,6 +105,9 @@ class AssetReference(Base):
     last_access_time: Mapped[datetime] = mapped_column(
         DateTime(timezone=False), nullable=False, default=get_utc_now
     )
+    deleted_at: Mapped[datetime | None] = mapped_column(
+        DateTime(timezone=False), nullable=True, default=None
+    )
 
     asset: Mapped[Asset] = relationship(
         "Asset",
@@ -148,6 +151,7 @@ class AssetReference(Base):
         Index("ix_asset_references_enrichment_level", "enrichment_level"),
         Index("ix_asset_references_created_at", "created_at"),
         Index("ix_asset_references_last_access_time", "last_access_time"),
+        Index("ix_asset_references_deleted_at", "deleted_at"),
         Index("ix_asset_references_owner_name", "owner_id", "name"),
         CheckConstraint(
             "(mtime_ns IS NULL) OR (mtime_ns >= 0)", name="ck_ar_mtime_nonneg"