refactor: migrate to Turborepo + pnpm + Biome monorepo

Restructure into apps/worker, apps/cli, packages/mcp-server with
Turborepo task orchestration, pnpm workspaces, Biome linting/formatting,
and tsdown CLI bundling.

Key changes:
- src/ -> apps/worker/src/, cli/ -> apps/cli/, mcp-server/ -> packages/mcp-server/
- prompts/ and configs/ moved into apps/worker/
- npm replaced with pnpm, package-lock.json replaced with pnpm-lock.yaml
- Dockerfile updated for pnpm-based builds
- CLI logs command rewritten with chokidar for cross-platform reliability
- Router health checking added for auto-detected router mode
- Centralized path resolution via apps/worker/src/paths.ts

packages/mcp-server/src/utils/error-formatter.ts

@@ -0,0 +1,67 @@
+// Copyright (C) 2025 Keygraph, Inc.
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License version 3
+// as published by the Free Software Foundation.
+
+/**
+ * Error Formatting Utilities
+ *
+ * Helper functions for creating structured error responses.
+ */
+
+import type { ErrorResponse } from '../types/tool-responses.js';
+
+/**
+ * Create a validation error response
+ */
+export function createValidationError(
+  message: string,
+  retryable: boolean = true,
+  context?: Record<string, unknown>,
+): ErrorResponse {
+  return {
+    status: 'error',
+    message,
+    errorType: 'ValidationError',
+    retryable,
+    ...(context !== undefined && { context }),
+  };
+}
+
+/**
+ * Create a crypto error response
+ */
+export function createCryptoError(
+  message: string,
+  retryable: boolean = false,
+  context?: Record<string, unknown>,
+): ErrorResponse {
+  return {
+    status: 'error',
+    message,
+    errorType: 'CryptoError',
+    retryable,
+    ...(context !== undefined && { context }),
+  };
+}
+
+/**
+ * Create a generic error response
+ */
+export function createGenericError(
+  error: unknown,
+  retryable: boolean = false,
+  context?: Record<string, unknown>,
+): ErrorResponse {
+  const message = error instanceof Error ? error.message : String(error);
+  const errorType = error instanceof Error ? error.constructor.name : 'UnknownError';
+
+  return {
+    status: 'error',
+    message,
+    errorType,
+    retryable,
+    ...(context !== undefined && { context }),
+  };
+}

packages/mcp-server/src/utils/file-operations.ts

@@ -0,0 +1,39 @@
+// Copyright (C) 2025 Keygraph, Inc.
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License version 3
+// as published by the Free Software Foundation.
+
+/**
+ * File Operations Utilities
+ *
+ * Handles file system operations for deliverable saving.
+ * Ported from tools/save_deliverable.js (lines 117-130).
+ */
+
+import { mkdirSync, writeFileSync } from 'node:fs';
+import { join } from 'node:path';
+
+/**
+ * Save deliverable file to deliverables/ directory
+ *
+ * @param targetDir - Target directory for deliverables (passed explicitly to avoid race conditions)
+ * @param filename - Name of the deliverable file
+ * @param content - File content to save
+ */
+export function saveDeliverableFile(targetDir: string, filename: string, content: string): string {
+  const deliverablesDir = join(targetDir, 'deliverables');
+  const filepath = join(deliverablesDir, filename);
+
+  // Ensure deliverables directory exists
+  try {
+    mkdirSync(deliverablesDir, { recursive: true });
+  } catch {
+    throw new Error(`Cannot create deliverables directory at ${deliverablesDir}`);
+  }
+
+  // Write file (atomic write - single operation)
+  writeFileSync(filepath, content, 'utf8');
+
+  return filepath;
+}