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/04-项目结构.md

@@ -41,7 +41,7 @@ Agentsd/
 │               ├── hid.rs
 │               └── input.rs
 │
-├── data/                          # 运行时数据(程序启动后自动创建)
+├── data/                          # 运行时数据(实际位于可执行文件旁,即 target/debug|release/data/)
 │   ├── memory.db                  # Memory syscall SQLite 数据库
 │   └── plugins.json               # 插件注册状态
 │
@@ -51,19 +51,28 @@ Agentsd/
     │   ├── agentsd_pb2.py
     │   └── agentsd_pb2_grpc.py
     │
+    ├── plugin-sdk/                # Rust 插件 SDK crate(连接/注册/元数据辅助)
+    │   ├── Cargo.toml
+    │   └── src/lib.rs
+    │
     ├── echo/                      # 测试插件(Rust)
+    │   ├── Cargo.toml
     │   ├── plugin.yaml
     │   └── src/main.rs
     │
     ├── ai_test/                   # AI 手动验证插件(Rust,enabled=false,autoload=false)
+    │   ├── Cargo.toml
     │   ├── plugin.yaml
     │   └── src/main.rs
     │
-    ├── hermes/                    # Hermes Agent 桥接(Python,Rust 版仅 stub)
+    ├── hermes/                    # Hermes Agent 桥接(Python 桥接工具注册表;Rust 版提供 echo 验证路由)
+    │   ├── Cargo.toml
     │   ├── plugin.yaml
-    │   └── hermes_plugin.py
+    │   ├── hermes_plugin.py
+    │   └── src/main.rs
     │
     └── claudecode/                # Claude Code CLI 桥接(Rust)
+        ├── Cargo.toml
         ├── plugin.yaml
         └── src/main.rs
 ```
@@ -114,3 +123,5 @@ python -m grpc_tools.protoc \
   --grpc_python_out=plugins/_sdk \
   proto/agentsd.proto
 ```
+
+注:protoc 只生成 `agentsd_pb2.py` 和 `agentsd_pb2_grpc.py`;`plugins/_sdk/__init__.py` 是手工维护的包标记文件,重新生成后不要删除。