refactor(src): 重构路径引用并重命名部分模块

- 统一调整内部模块导入路径，移除多余的 system 子目录
- 重命名 common/runtime/state.ts 为 common/state.ts 并同步更新相关引用
- 重命名 common/runtime/validate.ts 为 common/validate.ts 并同步更新相关引用
- 重命名 common/runtime/file-history.ts 为 common/file-history 并同步更新相关引用
- 更新测试文件和工具模块中对应的导入路径，确保一致性
- 保持代码逻辑不变，仅调整代码结构和模块路径优化维护性

Author: hqwlkj

src/cli.tsx

@@ -1,6 +1,6 @@
 import React from "react";
 import { render } from "ink";
-import { setShellIfWindows } from "./common/system/shell-utils";
+import { setShellIfWindows } from "./common/shell-utils";
 import { checkForNpmUpdate, promptForPendingUpdate, type PackageInfo } from "./common/update-check";
 import { AppContainer } from "./ui";
 

src/common/system/bash-timeout.ts src/common/bash-timeout.tssrc/common/system/bash-timeout.ts renamed to src/common/bash-timeout.ts

@@ -1,6 +1,6 @@
 import * as fs from "fs";
 import * as path from "path";
-import type { FileState, FileLineEnding } from "./runtime/state";
+import type { FileState, FileLineEnding } from "./state";
 
 export type FileReadMetadata = {
   content: string;

src/common/logging/debug-logger.ts src/common/debug-logger.tssrc/common/logging/debug-logger.ts renamed to src/common/debug-logger.ts

@@ -1,7 +1,7 @@
 import * as fs from "fs";
 import * as path from "path";
 import type { DeepcodingSettings, PermissionScope, PermissionSettings } from "../settings";
-import { isAbsoluteFilePath, normalizeFilePath } from "./runtime/state";
+import { isAbsoluteFilePath, normalizeFilePath } from "./state";
 
 export type BashPermissionScope = Exclude<PermissionScope, "mcp"> | "unknown";
 

src/common/logging/error-logger.ts src/common/error-logger.tssrc/common/logging/error-logger.ts renamed to src/common/error-logger.ts

@@ -1,5 +1,5 @@
 import * as path from "path";
-import { posixPathToWindowsPath } from "../system/shell-utils";
+import { posixPathToWindowsPath } from "./shell-utils";
 
 export type FileLineEnding = "LF" | "CRLF";