docs(mvp): update RAG docs for py-rag extraction

- rewrite RAG architecture doc for py-rag service contract mapping, ingest and rebuild ops
- refresh observability/trace doc for post-L0 single-attempt semantics
- add py-rag chain exploration note; mark superseded Milvus/L0 notes with status banners
- close ISS-017 (superseded by L0 sinking); mark knowledge_domain table orphaned
- refresh architecture/mvp/engineering indexes

mvp/engineering/diagnosis/一次诊断全流程-E2E导读.md

@@ -4,6 +4,10 @@
 **状态**：SUCCESS 完整诊断主文档；工具阶段按**现行**审计能力（`step_id` / `query`）说明  
 **文档路径**：`mvp/engineering/diagnosis/一次诊断全流程-E2E导读.md`
 
+> **现状说明（2026-09-29）**：本文基于 2026-07 的 live Run 编写，图中 `VectorSearchService` /
+> `MilvusHybridKnowledgeStore`（进程内 Milvus）已替换为 py-rag 服务调用；审计/Trace 结构不变。
+> 当前检索链路见 [../architecture/RAG知识检索架构.md](../architecture/RAG知识检索架构.md)。
+
 ### 主样本（正文数值与 timeline 来源）
 
 | 项 | 值 |