Summary

manage_prefabs fails to save prefab-stage edits because save_prefab_stage appears to save the prefab preview scene with scene-save APIs instead of writing the prefab asset itself.

Error

Error saving prefab stage: EditorSceneManager.SetActive failed; you can not save a preview scene

Minimal Repro

1. Open any prefab through manage_prefabs(action="open_prefab_stage", prefab_path="Assets/.../Example.prefab").
2. Make a simple change inside the prefab stage, such as adding a child GameObject.
3. Call manage_prefabs(action="save_prefab_stage").
4. Observe the save failure instead of the prefab asset being persisted.

Likely Root Cause

save_prefab_stage appears to use scene-save APIs on a prefab preview scene. In MCPForUnity/Editor/Tools/Prefabs/ManagePrefabs.cs, the current implementation marks prefabStage.scene dirty and then calls EditorSceneManager.SaveScene(prefabStage.scene), but prefab stages use preview scenes rather than normal savable editor scenes.

The prefab-stage save path likely needs to use the prefab asset workflow instead (for example, saving prefabStage.prefabContentsRoot back to prefabStage.assetPath) and close_prefab_stage(saveBeforeClose: true) should reuse the same path.