feat: implement CI (Continuous Intelligence) autonomous engineering harness

Implements the full PRD for CI - a fully autonomous AI-driven software
engineering harness derived from Learnship's architecture.

Core components:
- CI Orchestrator agent with autonomous pipeline (SPECIFY → CLARIFY →
  RESEARCH → PLAN → EXECUTE → VERIFY → COMPLETE)
- Decision Engine with confidence thresholds (high/medium/low)
- Clarify Phase with question budget and default acceptance
- Escalation Protocol with timeout auto-proceed
- Audit Trail system (.ci/audit/) for post-hoc review
- Error Recovery with retry, plan revision, and rollback

18 agents (all Learnship agents + Orchestrator):
- Autonomous behavioral modifications per PRD §7.1
- Agent registry with factory pattern

11 CLI commands:
- ci init, ci run, ci quick, ci debug, ci verify
- ci review, ci status, ci audit, ci clarify
- ci rollback, ci ship

4-layer verification system:
- Structural, Behavioral, Security, Code Quality

3 autonomy levels: full, supervised, guided
Compatible with Learnship artifact schemas (.planning/)

src/utils/file.ts

@@ -0,0 +1,56 @@
+import * as fs from "node:fs";
+import * as path from "node:path";
+
+export function fileExists(filePath: string): boolean {
+  return fs.existsSync(filePath);
+}
+
+export function ensureDir(dirPath: string): void {
+  if (!fs.existsSync(dirPath)) {
+    fs.mkdirSync(dirPath, { recursive: true });
+  }
+}
+
+export function readFile(filePath: string): string | null {
+  if (!fs.existsSync(filePath)) return null;
+  return fs.readFileSync(filePath, "utf-8");
+}
+
+export function writeFile(filePath: string, content: string): void {
+  const dir = path.dirname(filePath);
+  ensureDir(dir);
+  fs.writeFileSync(filePath, content, "utf-8");
+}
+
+export function readJSON<T>(filePath: string): T | null {
+  const content = readFile(filePath);
+  if (!content) return null;
+  return JSON.parse(content) as T;
+}
+
+export function writeJSON(filePath: string, data: unknown): void {
+  writeFile(filePath, JSON.stringify(data, null, 2));
+}
+
+export function listFiles(dirPath: string, pattern?: RegExp): string[] {
+  if (!fs.existsSync(dirPath)) return [];
+  const files = fs.readdirSync(dirPath);
+  if (pattern) return files.filter((f) => pattern.test(f));
+  return files;
+}
+
+export function copyFile(src: string, dest: string): void {
+  ensureDir(path.dirname(dest));
+  fs.copyFileSync(src, dest);
+}
+
+export function getProjectRoot(startPath?: string): string {
+  let current = startPath || process.cwd();
+  while (current !== path.dirname(current)) {
+    if (fs.existsSync(path.join(current, ".ci"))) return current;
+    if (fs.existsSync(path.join(current, ".git"))) return current;
+    if (fs.existsSync(path.join(current, "package.json"))) return current;
+    current = path.dirname(current);
+  }
+  return startPath || process.cwd();
+}

src/utils/index.ts

@@ -0,0 +1 @@
+export * from "./file.js";