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/tests/unit/lib/security.test.ts

@@ -129,16 +129,38 @@ describe("security.ts", () => {
   });
 
   describe("isPathAllowed", () => {
-    it("should allow all paths (permissions disabled)", async () => {
+    it("should allow paths within configured allowed directories", async () => {
       process.env.ALLOWED_PROJECT_DIRS = "/allowed/project";
       process.env.DATA_DIR = "";
+      delete process.env.ALLOWED_ROOT_DIRECTORY;
 
       const { initAllowedPaths, isPathAllowed } = await import(
         "@/lib/security.js"
       );
       initAllowedPaths();
 
-      // All paths are now allowed regardless of configuration
+      // Paths within allowed directory should be allowed
+      expect(isPathAllowed("/allowed/project/file.txt")).toBe(true);
+      expect(isPathAllowed("/allowed/project/subdir/file.txt")).toBe(true);
+
+      // Paths outside allowed directory should be denied
+      expect(isPathAllowed("/not/allowed/file.txt")).toBe(false);
+      expect(isPathAllowed("/tmp/file.txt")).toBe(false);
+      expect(isPathAllowed("/etc/passwd")).toBe(false);
+    });
+
+    it("should allow all paths when no restrictions are configured", async () => {
+      delete process.env.ALLOWED_PROJECT_DIRS;
+      delete process.env.DATA_DIR;
+      delete process.env.WORKSPACE_DIR;
+      delete process.env.ALLOWED_ROOT_DIRECTORY;
+
+      const { initAllowedPaths, isPathAllowed } = await import(
+        "@/lib/security.js"
+      );
+      initAllowedPaths();
+
+      // All paths should be allowed when no restrictions are configured
       expect(isPathAllowed("/allowed/project/file.txt")).toBe(true);
       expect(isPathAllowed("/not/allowed/file.txt")).toBe(true);
       expect(isPathAllowed("/tmp/file.txt")).toBe(true);
@@ -148,9 +170,10 @@ describe("security.ts", () => {
   });
 
   describe("validatePath", () => {
-    it("should return resolved path for any path (permissions disabled)", async () => {
+    it("should return resolved path for allowed paths", async () => {
       process.env.ALLOWED_PROJECT_DIRS = "/allowed";
       process.env.DATA_DIR = "";
+      delete process.env.ALLOWED_ROOT_DIRECTORY;
 
       const { initAllowedPaths, validatePath } = await import(
         "@/lib/security.js"
@@ -161,26 +184,43 @@ describe("security.ts", () => {
       expect(result).toBe(path.resolve("/allowed/file.txt"));
     });
 
-    it("should not throw error for any path (permissions disabled)", async () => {
+    it("should throw error for paths outside allowed directories", async () => {
       process.env.ALLOWED_PROJECT_DIRS = "/allowed";
       process.env.DATA_DIR = "";
+      delete process.env.ALLOWED_ROOT_DIRECTORY;
 
       const { initAllowedPaths, validatePath } = await import(
         "@/lib/security.js"
       );
       initAllowedPaths();
 
-      // All paths are now allowed, no errors thrown
+      // Disallowed paths should throw PathNotAllowedError
+      expect(() => validatePath("/disallowed/file.txt")).toThrow();
+    });
+
+    it("should not throw error for any path when no restrictions are configured", async () => {
+      delete process.env.ALLOWED_PROJECT_DIRS;
+      delete process.env.DATA_DIR;
+      delete process.env.WORKSPACE_DIR;
+      delete process.env.ALLOWED_ROOT_DIRECTORY;
+
+      const { initAllowedPaths, validatePath } = await import(
+        "@/lib/security.js"
+      );
+      initAllowedPaths();
+
+      // All paths are allowed when no restrictions configured
       expect(() => validatePath("/disallowed/file.txt")).not.toThrow();
       expect(validatePath("/disallowed/file.txt")).toBe(
         path.resolve("/disallowed/file.txt")
       );
     });
 
-    it("should resolve relative paths", async () => {
+    it("should resolve relative paths within allowed directory", async () => {
       const cwd = process.cwd();
       process.env.ALLOWED_PROJECT_DIRS = cwd;
       process.env.DATA_DIR = "";
+      delete process.env.ALLOWED_ROOT_DIRECTORY;
 
       const { initAllowedPaths, validatePath } = await import(
         "@/lib/security.js"