Clear (soft-archive) a persisted edit

Clear an edit — sets cleared_at and removes it from future overlays.

For ADD edits with a corresponding user-prompt stored on ContextDocConfig.prompts[tier][key], also clear that prompt so the prompts UI doesn't dangle an entry for a file that no longer exists.

Keeps the row around for audit. To restore, the user re-creates the edit via PATCH /files.