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/types/pipeline.ts

@@ -0,0 +1,92 @@
+import { AgentName, PhaseName } from "./config.js";
+
+export type PipelineStage =
+  | "specify"
+  | "clarify"
+  | "research"
+  | "plan"
+  | "execute"
+  | "verify"
+  | "complete";
+
+export interface PipelineState {
+  project_path: string;
+  current_stage: PipelineStage;
+  current_phase: number;
+  phases_completed: number[];
+  specification_loaded: boolean;
+  clarify_completed: boolean;
+  research_completed: boolean;
+  plan_completed: boolean;
+  execute_completed: boolean;
+  verify_completed: boolean;
+  errors: PipelineError[];
+  started_at: string;
+  last_updated: string;
+}
+
+export interface PipelineError {
+  stage: PipelineStage;
+  phase: number;
+  message: string;
+  timestamp: string;
+  retry_count: number;
+  resolved: boolean;
+}
+
+export interface PhaseResult {
+  phase: number;
+  stage: PipelineStage;
+  success: boolean;
+  artifacts_created: string[];
+  decisions_made: number;
+  escalations_raised: number;
+  duration_ms: number;
+  error?: string;
+}
+
+export interface OrchestratorResult {
+  success: boolean;
+  pipeline_state: PipelineState;
+  phase_results: PhaseResult[];
+  total_decisions: number;
+  total_escalations: number;
+  total_duration_ms: number;
+  completion_report: string;
+}
+
+export const STAGE_ORDER: PipelineStage[] = [
+  "specify",
+  "clarify",
+  "research",
+  "plan",
+  "execute",
+  "verify",
+  "complete",
+];
+
+export function getNextStage(current: PipelineStage): PipelineStage | null {
+  const idx = STAGE_ORDER.indexOf(current);
+  if (idx < 0 || idx >= STAGE_ORDER.length - 1) return null;
+  return STAGE_ORDER[idx + 1];
+}
+
+export function createInitialPipelineState(
+  project_path: string
+): PipelineState {
+  return {
+    project_path,
+    current_stage: "specify",
+    current_phase: 0,
+    phases_completed: [],
+    specification_loaded: false,
+    clarify_completed: false,
+    research_completed: false,
+    plan_completed: false,
+    execute_completed: false,
+    verify_completed: false,
+    errors: [],
+    started_at: new Date().toISOString(),
+    last_updated: new Date().toISOString(),
+  };
+}