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/core/config.ts

@@ -0,0 +1,65 @@
+import * as fs from "node:fs";
+import * as path from "node:path";
+import { CIConfig, DEFAULT_CI_CONFIG } from "../types/config.js";
+
+const CI_DIR = ".ci";
+const CONFIG_FILE = "config.json";
+
+export function getCIConfigPath(projectPath: string): string {
+  return path.join(projectPath, CI_DIR, CONFIG_FILE);
+}
+
+export function getCIDir(projectPath: string): string {
+  return path.join(projectPath, CI_DIR);
+}
+
+export function ensureCIDir(projectPath: string): void {
+  const ciDir = getCIDir(projectPath);
+  if (!fs.existsSync(ciDir)) {
+    fs.mkdirSync(ciDir, { recursive: true });
+  }
+  const auditDir = path.join(ciDir, "audit");
+  if (!fs.existsSync(auditDir)) {
+    fs.mkdirSync(auditDir, { recursive: true });
+  }
+}
+
+export function loadConfig(projectPath: string): CIConfig {
+  const configPath = getCIConfigPath(projectPath);
+  if (!fs.existsSync(configPath)) {
+    return { ...DEFAULT_CI_CONFIG };
+  }
+  const raw = fs.readFileSync(configPath, "utf-8");
+  const parsed = JSON.parse(raw);
+  return { ...DEFAULT_CI_CONFIG, ...parsed } as CIConfig;
+}
+
+export function saveConfig(projectPath: string, config: CIConfig): void {
+  ensureCIDir(projectPath);
+  const configPath = getCIConfigPath(projectPath);
+  fs.writeFileSync(configPath, JSON.stringify(config, null, 2), "utf-8");
+}
+
+export function isCIInitialized(projectPath: string): boolean {
+  const ciDir = getCIDir(projectPath);
+  const configPath = getCIConfigPath(projectPath);
+  return fs.existsSync(ciDir) && fs.existsSync(configPath);
+}
+
+export function initCI(projectPath: string, config?: Partial<CIConfig>): CIConfig {
+  ensureCIDir(projectPath);
+  const fullConfig: CIConfig = {
+    ...DEFAULT_CI_CONFIG,
+    ...config,
+    autonomy: { ...DEFAULT_CI_CONFIG.autonomy, ...config?.autonomy },
+    parallelization: {
+      ...DEFAULT_CI_CONFIG.parallelization,
+      ...config?.parallelization,
+    },
+    verification: { ...DEFAULT_CI_CONFIG.verification, ...config?.verification },
+    security: { ...DEFAULT_CI_CONFIG.security, ...config?.security },
+    git: { ...DEFAULT_CI_CONFIG.git, ...config?.git },
+  };
+  saveConfig(projectPath, fullConfig);
+  return fullConfig;
+}