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>

README.md

@@ -2,7 +2,7 @@
 
 AI Agent 的 init 系统 + 内核。对标 Linux 内核 + systemd。
 
-> 状态:设计草案
+> 状态:阶段 1(内核骨架)已完成,阶段 2/3 部分完成。详见 docs/03-实施路线.md
 
 ## 对标