Fix history mismatch

Set the properties of the resource's proxy instead of setting the resource's
properties directly. (For action "Set ...")

Update the path of the edited scene when saving the scene. (For action "Add
atlas source")

(cherry picked from commit 28db5e76495bab5f0cb3fa4a4b7d4769d25c9962)

editor/editor_node.cpp

@@ -1982,6 +1982,9 @@ void EditorNode::_dialog_action(String p_file) {
 
 				if (scene_idx != -1) {
 					_discard_changes();
+				} else {
+					// Update the path of the edited scene to ensure later do/undo action history matches.
+					editor_data.set_scene_path(editor_data.get_edited_scene(), p_file);
 				}
 			}
 

editor/plugins/tiles/tile_set_atlas_source_editor.cpp

@@ -2156,7 +2156,7 @@ void TileSetAtlasSourceEditor::_undo_redo_inspector_callback(Object *p_undo_redo
 		Ref<TileSetAtlasSource> atlas_source = atlas_source_proxy->get_edited();
 		ERR_FAIL_COND(!atlas_source.is_valid());
 
-		UndoRedo *internal_undo_redo = undo_redo_man->get_history_for_object(atlas_source.ptr()).undo_redo;
+		UndoRedo *internal_undo_redo = undo_redo_man->get_history_for_object(atlas_source_proxy).undo_redo;
 		internal_undo_redo->start_force_keep_in_merge_ends();
 
 		PackedVector2Array arr;
@@ -2180,7 +2180,7 @@ void TileSetAtlasSourceEditor::_undo_redo_inspector_callback(Object *p_undo_redo
 				String prefix = vformat("%d:%d/", coords.x, coords.y);
 				for (PropertyInfo pi : properties) {
 					if (pi.name.begins_with(prefix)) {
-						ADD_UNDO(atlas_source.ptr(), pi.name);
+						ADD_UNDO(atlas_source_proxy, pi.name);
 					}
 				}
 			}