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/cli/index.ts

@@ -0,0 +1,37 @@
+#!/usr/bin/env node
+
+import { Command } from "commander";
+import { VERSION } from "../version.js";
+import {
+  createInitCommand,
+  createRunCommand,
+  createQuickCommand,
+  createDebugCommand,
+  createVerifyCommand,
+  createReviewCommand,
+  createStatusCommand,
+  createAuditCommand,
+  createClarifyCommand,
+  createRollbackCommand,
+  createShipCommand,
+} from "./commands.js";
+
+const program = new Command();
+
+program
+  .name("ci")
+  .description("CI — Continuous Intelligence: autonomous AI-driven software engineering harness")
+  .version(VERSION)
+  .addCommand(createInitCommand())
+  .addCommand(createRunCommand())
+  .addCommand(createQuickCommand())
+  .addCommand(createDebugCommand())
+  .addCommand(createVerifyCommand())
+  .addCommand(createReviewCommand())
+  .addCommand(createStatusCommand())
+  .addCommand(createAuditCommand())
+  .addCommand(createClarifyCommand())
+  .addCommand(createRollbackCommand())
+  .addCommand(createShipCommand());
+
+program.parse();