feat: implement secure file system access and path validation

- Introduced a restricted file system wrapper to ensure all file operations are confined to the script's directory, enhancing security.
- Updated various modules to utilize the new secure file system methods, replacing direct fs calls with validated operations.
- Enhanced path validation in the server routes and context loaders to prevent unauthorized access to the file system.
- Adjusted environment variable handling to use centralized methods for reading and writing API keys, ensuring consistent security practices.

This change improves the overall security posture of the application by enforcing strict file access controls and validating paths before any operations are performed.

apps/server/src/routes/setup/common.ts

@@ -4,7 +4,7 @@
 
 import { createLogger } from '@automaker/utils';
 import path from 'path';
-import fs from 'fs/promises';
+import { secureFs } from '@automaker/platform';
 import { getErrorMessage as getErrorMessageShared, createLogError } from '../common.js';
 
 const logger = createLogger('Setup');
@@ -35,36 +35,13 @@ export function getAllApiKeys(): Record<string, string> {
 
 /**
  * Helper to persist API keys to .env file
+ * Uses centralized secureFs.writeEnvKey for path validation
  */
 export async function persistApiKeyToEnv(key: string, value: string): Promise<void> {
   const envPath = path.join(process.cwd(), '.env');
 
   try {
-    let envContent = '';
-    try {
-      envContent = await fs.readFile(envPath, 'utf-8');
-    } catch {
-      // .env file doesn't exist, we'll create it
-    }
-
-    // Parse existing env content
-    const lines = envContent.split('\n');
-    const keyRegex = new RegExp(`^${key}=`);
-    let found = false;
-    const newLines = lines.map((line) => {
-      if (keyRegex.test(line)) {
-        found = true;
-        return `${key}=${value}`;
-      }
-      return line;
-    });
-
-    if (!found) {
-      // Add the key at the end
-      newLines.push(`${key}=${value}`);
-    }
-
-    await fs.writeFile(envPath, newLines.join('\n'));
+    await secureFs.writeEnvKey(envPath, key, value);
     logger.info(`[Setup] Persisted ${key} to .env file`);
   } catch (error) {
     logger.error(`[Setup] Failed to persist ${key} to .env:`, error);