Fix documentation inconsistencies found by code audit

- docs/01: sync all syscall signatures with proto (missing params,
  invented callback params, stream semantics, return types)
- docs/02: mark unimplemented features (FFI system plugins, topo sort,
  lifecycle CLI, watchdog); clarify plugin.yaml is not parsed by the
  kernel - registration goes through gRPC PluginBridge.Register;
  correct permission model and session_id descriptions
- docs/03: check off implemented stage 3 items (Hermes adapter,
  Claude Code plugin)
- docs/04: data/ actual location, add Cargo.toml to plugin trees,
  note __init__.py is hand-maintained
- README: status line now reflects actual progress

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

docs/03-实施路线.md

@@ -23,7 +23,7 @@
 
 **验证结果**:agentsd 启动 → Rust 插件通过 gRPC 注册 → ai_test 调用 Display/Memory/FS/Process/Timer syscall 并验证权限拒绝。
 
-## 阶段 2:完善核心 syscall ✅ 部分完成
+## 阶段 2:完善核心 syscall 🔶 部分完成
 
 - [x] Network:reqwest 原生 HTTP client(阶段 1 已完成)
 - [x] Network TCP 流:open_conn/send/close/listen 双向 TCP 通信
@@ -33,10 +33,11 @@
 - [ ] HID:接入屏幕截取(Windows: win32 API)
 - [ ] Unix socket / Named pipe 传输(替代 TCP)
 
-## 阶段 3:接入 Agent
+## 阶段 3:接入 Agent 🔶 部分完成
 
 - [ ] Agent 插件:Input → LLM(Network) → Display
-- [ ] Hermes adapter(Python gRPC 插件)
+- [x] Hermes adapter:`hermes_plugin.py` 桥接 Hermes 工具注册表;Rust 版 hermes 插件提供 echo 验证路由,bridge.call 路由已验证
+- [x] Claude Code 插件(Rust,standard 类型,depends: hermes,导出 chat/code/review/ask/run)
 - [ ] 本地模型插件(llama.cpp via Process syscall)
 
 ## 阶段 4:插件管理(= systemctl)