refactor: streamline ALLOWED_ROOT_DIRECTORY handling and remove legacy support

This commit refactors the handling of ALLOWED_ROOT_DIRECTORY by removing legacy support for ALLOWED_PROJECT_DIRS and simplifying the security logic. Key changes include:

- Removed deprecated ALLOWED_PROJECT_DIRS references from .env.example and security.ts.
- Updated initAllowedPaths() to focus solely on ALLOWED_ROOT_DIRECTORY and DATA_DIR.
- Enhanced logging for ALLOWED_ROOT_DIRECTORY configuration status.
- Adjusted route handlers to utilize the new workspace directory logic.
- Introduced a centralized storage module for localStorage operations to improve consistency and error handling.

These changes aim to enhance security and maintainability by consolidating directory management into a single variable.

Tests: All unit tests passing.

apps/server/tests/setup.ts

@@ -8,7 +8,6 @@ import { vi, beforeEach } from "vitest";
 // Set test environment variables
 process.env.NODE_ENV = "test";
 process.env.DATA_DIR = "/tmp/test-data";
-process.env.ALLOWED_PROJECT_DIRS = "/tmp/test-projects";
 
 // Reset all mocks before each test
 beforeEach(() => {