pipeline: opt out of copy-on-write for objects

When committing an object to the store, clone it if the current
stage is not the latests stage, i.e. `todo` has still entries.
This is the second step of the removal of copy-on-write support
in `Object`.

osbuild/pipeline.py

@@ -359,7 +359,7 @@ class Pipeline:
             tree.id = stage.id
 
             if stage.checkpoint:
-                object_store.commit(tree, stage.id)
+                object_store.commit(tree, stage.id, clone=bool(todo))
 
         return results