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/routes/git/index.ts

@@ -3,14 +3,15 @@
  */
 
 import { Router } from "express";
+import { validatePathParams } from "../../middleware/validate-paths.js";
 import { createDiffsHandler } from "./routes/diffs.js";
 import { createFileDiffHandler } from "./routes/file-diff.js";
 
 export function createGitRoutes(): Router {
   const router = Router();
 
-  router.post("/diffs", createDiffsHandler());
-  router.post("/file-diff", createFileDiffHandler());
+  router.post("/diffs", validatePathParams("projectPath"), createDiffsHandler());
+  router.post("/file-diff", validatePathParams("projectPath", "filePath"), createFileDiffHandler());
 
   return router;
 }