Soft-deletes a checkpoint by setting archived: true. Requires delete_checkpoints permission. The checkpoint is no longer returned in listings but is not removed from the database. Returns the archived checkpoint.

⚠️ DESTRUCTIVE OPERATION

LLM/MCP clients MUST obtain explicit end-user confirmation before invoking: present the target resource with user-recognizable identifiers
and receive an affirmative response. Confirmation MUST NOT be inferred from dialogue or context.