refactor: integrate secure file system operations across services

This commit replaces direct file system operations with a secure file system adapter to enhance security by enforcing path validation. The changes include:

- Replaced `fs` imports with `secureFs` in various services and utilities.
- Updated file operations in `agent-service`, `auto-mode-service`, `feature-loader`, and `settings-service` to use the secure file system methods.
- Ensured that all file I/O operations are validated against the ALLOWED_ROOT_DIRECTORY.

This refactor aims to prevent unauthorized file access and improve overall security posture.

Tests: All unit tests passing.

🤖 Generated with Claude Code

apps/server/src/lib/secure-fs.ts

@@ -0,0 +1,156 @@
+/**
+ * Secure File System Adapter
+ *
+ * All file I/O operations must go through this adapter to enforce
+ * ALLOWED_ROOT_DIRECTORY restrictions at the actual access point,
+ * not just at the API layer. This provides defense-in-depth security.
+ */
+
+import fs from "fs/promises";
+import path from "path";
+import { validatePath } from "./security.js";
+
+/**
+ * Wrapper around fs.access that validates path first
+ */
+export async function access(filePath: string, mode?: number): Promise<void> {
+  const validatedPath = validatePath(filePath);
+  return fs.access(validatedPath, mode);
+}
+
+/**
+ * Wrapper around fs.readFile that validates path first
+ */
+export async function readFile(
+  filePath: string,
+  encoding?: BufferEncoding
+): Promise<string | Buffer> {
+  const validatedPath = validatePath(filePath);
+  if (encoding) {
+    return fs.readFile(validatedPath, encoding);
+  }
+  return fs.readFile(validatedPath);
+}
+
+/**
+ * Wrapper around fs.writeFile that validates path first
+ */
+export async function writeFile(
+  filePath: string,
+  data: string | Buffer,
+  encoding?: BufferEncoding
+): Promise<void> {
+  const validatedPath = validatePath(filePath);
+  return fs.writeFile(validatedPath, data, encoding as any);
+}
+
+/**
+ * Wrapper around fs.mkdir that validates path first
+ */
+export async function mkdir(
+  dirPath: string,
+  options?: { recursive?: boolean; mode?: number }
+): Promise<string | undefined> {
+  const validatedPath = validatePath(dirPath);
+  return fs.mkdir(validatedPath, options);
+}
+
+/**
+ * Wrapper around fs.readdir that validates path first
+ */
+export async function readdir(
+  dirPath: string,
+  options?: { withFileTypes?: boolean; encoding?: BufferEncoding }
+): Promise<string[] | any[]> {
+  const validatedPath = validatePath(dirPath);
+  return fs.readdir(validatedPath, options as any);
+}
+
+/**
+ * Wrapper around fs.stat that validates path first
+ */
+export async function stat(filePath: string): Promise<any> {
+  const validatedPath = validatePath(filePath);
+  return fs.stat(validatedPath);
+}
+
+/**
+ * Wrapper around fs.rm that validates path first
+ */
+export async function rm(
+  filePath: string,
+  options?: { recursive?: boolean; force?: boolean }
+): Promise<void> {
+  const validatedPath = validatePath(filePath);
+  return fs.rm(validatedPath, options);
+}
+
+/**
+ * Wrapper around fs.unlink that validates path first
+ */
+export async function unlink(filePath: string): Promise<void> {
+  const validatedPath = validatePath(filePath);
+  return fs.unlink(validatedPath);
+}
+
+/**
+ * Wrapper around fs.copyFile that validates both paths first
+ */
+export async function copyFile(
+  src: string,
+  dest: string,
+  mode?: number
+): Promise<void> {
+  const validatedSrc = validatePath(src);
+  const validatedDest = validatePath(dest);
+  return fs.copyFile(validatedSrc, validatedDest, mode);
+}
+
+/**
+ * Wrapper around fs.appendFile that validates path first
+ */
+export async function appendFile(
+  filePath: string,
+  data: string | Buffer,
+  encoding?: BufferEncoding
+): Promise<void> {
+  const validatedPath = validatePath(filePath);
+  return fs.appendFile(validatedPath, data, encoding as any);
+}
+
+/**
+ * Wrapper around fs.rename that validates both paths first
+ */
+export async function rename(
+  oldPath: string,
+  newPath: string
+): Promise<void> {
+  const validatedOldPath = validatePath(oldPath);
+  const validatedNewPath = validatePath(newPath);
+  return fs.rename(validatedOldPath, validatedNewPath);
+}
+
+/**
+ * Wrapper around fs.lstat that validates path first
+ * Returns file stats without following symbolic links
+ */
+export async function lstat(filePath: string): Promise<any> {
+  const validatedPath = validatePath(filePath);
+  return fs.lstat(validatedPath);
+}
+
+/**
+ * Wrapper around path.join that returns resolved path
+ * Does NOT validate - use this for path construction, then pass to other operations
+ */
+export function joinPath(...pathSegments: string[]): string {
+  return path.join(...pathSegments);
+}
+
+/**
+ * Wrapper around path.resolve that returns resolved path
+ * Does NOT validate - use this for path construction, then pass to other operations
+ */
+export function resolvePath(...pathSegments: string[]): string {
+  return path.resolve(...pathSegments);
+}