refactor: implement ALLOWED_ROOT_DIRECTORY security and fix path validation

This commit consolidates directory security from two environment variables
(WORKSPACE_DIR, ALLOWED_PROJECT_DIRS) into a single ALLOWED_ROOT_DIRECTORY variable
while maintaining backward compatibility.

Changes:
- Re-enabled path validation in security.ts (was previously disabled)
- Implemented isPathAllowed() to check ALLOWED_ROOT_DIRECTORY with DATA_DIR exception
- Added backward compatibility for legacy ALLOWED_PROJECT_DIRS and WORKSPACE_DIR
- Implemented path traversal protection via isPathWithinDirectory() helper
- Added PathNotAllowedError custom exception for security violations
- Updated all FS route endpoints to validate paths and return 403 on violation
- Updated template clone endpoint to validate project paths
- Updated workspace config endpoints to use ALLOWED_ROOT_DIRECTORY
- Fixed stat() response property access bug in project-init.ts
- Updated security tests to expect actual validation behavior

Security improvements:
- Path validation now enforced at all layers (routes, project init, agent services)
- appData directory (DATA_DIR) always allowed for settings/credentials
- Backward compatible with existing ALLOWED_PROJECT_DIRS/WORKSPACE_DIR configurations
- Protection against path traversal attacks

Backend test results: 654/654 passing ✅

🤖 Generated with Claude Code

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

apps/server/src/services/auto-mode-service.ts

@@ -24,6 +24,7 @@ import { resolveDependencies, areDependenciesSatisfied } from "../lib/dependency
 import type { Feature } from "./feature-loader.js";
 import { FeatureLoader } from "./feature-loader.js";
 import { getFeatureDir, getAutomakerDir, getFeaturesDir, getContextDir } from "../lib/automaker-paths.js";
+import { isPathAllowed, PathNotAllowedError } from "../lib/security.js";
 
 const execAsync = promisify(exec);
 
@@ -486,6 +487,11 @@ export class AutoModeService {
     this.runningFeatures.set(featureId, tempRunningFeature);
 
     try {
+      // Validate that project path is allowed
+      if (!isPathAllowed(projectPath)) {
+        throw new PathNotAllowedError(projectPath);
+      }
+
       // Check if feature has existing context - if so, resume instead of starting fresh
       // Skip this check if we're already being called with a continuation prompt (from resumeFeature)
       if (!options?.continuationPrompt) {
@@ -549,6 +555,11 @@ export class AutoModeService {
         ? path.resolve(worktreePath)
         : path.resolve(projectPath);
 
+      // Validate that working directory is allowed
+      if (!isPathAllowed(workDir)) {
+        throw new PathNotAllowedError(workDir);
+      }
+
       // Update running feature with actual worktree info
       tempRunningFeature.worktreePath = worktreePath;
       tempRunningFeature.branchName = branchName ?? null;