docs: remove outdated and unused documentation files

A significant number of documentation files, including design documents, user guides, and old images, have been removed to clean up the repository and eliminate outdated information. This reduces clutter and ensures that the documentation accurately reflects the current state of the project.

Key removals include:
- `memory_system_design_v3.md`
- `model_configuration_guide.md`
- `PERMISSION_SYSTEM.md`
- `CONTRIBUTE.md`
- `vector_db_usage_guide.md

src/plugin_system/core/tool_use.py

@@ -244,13 +244,14 @@ class ToolExecutor:
             function_name = tool_call.func_name
             function_args = tool_call.args or {}
             logger.info(f"{self.log_prefix} 正在执行工具: [bold green]{function_name}[/bold green] | 参数: {function_args}")
-            function_args["llm_called"] = True
-
+            function_args["llm_called"] = True  # 标记为LLM调用
+            # 获取对应工具实例
             tool_instance = tool_instance or get_tool_instance(function_name)
             if not tool_instance:
                 logger.warning(f"未知工具名称: {function_name}")
                 return None
 
+            # 执行工具并记录日志
             logger.debug(f"{self.log_prefix}执行工具 {function_name}，参数: {function_args}")
             result = await tool_instance.execute(function_args)
             if result: