Overhaul README.md to reflect Phase 12 complete architecture

Major updates:
- Architecture diagram: multi-agent pipeline with ALPHA/BETA/GAMMA agents
- Phase status: all 12 phases complete (295/295 tests)
- Added Vault token lifecycle documentation
- Added consensus failure handling workflows
- Added CLI reference: bugs, checkpoint, status, memory
- Added API endpoints documentation
- Added production constraints and revocation triggers
- Cross-linked to MULTI_AGENT_PIPELINE_ARCHITECTURE.md
- Created README_REFRESH_PLAN.md for tracking

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

docs/README_REFRESH_PLAN.md

@@ -0,0 +1,104 @@
+# README Refresh Plan
+
+**Created:** 2026-01-24 23:30 UTC
+**Status:** COMPLETE
+**Last Updated:** 2026-01-24 23:45 UTC
+
+---
+
+## Overview
+
+This document tracks the comprehensive documentation overhaul needed to bring the public repository in sync with the actual system state. The README was last updated during Phase 8; we are now at Phase 12 COMPLETE.
+
+## Gap Analysis
+
+| Area | README Says | Reality |
+|------|-------------|---------|
+| Phase | Phase 8 In Progress | Phase 12 COMPLETE |
+| Progress | 23% complete | 100% complete (295/295 tests) |
+| Architecture | Basic tiered agents | Full multi-agent pipeline with ALPHA/BETA/GAMMA |
+| UI | Not mentioned | Full orchestration dashboard with WebSocket |
+| Vault | Basic mention | Per-pipeline token lifecycle with observability revocation |
+| DragonflyDB | "state coordination" | Full observability, consensus tracking, metrics |
+| Consensus | Not mentioned | Consensus failure handling with fallback options |
+| Bug Tracking | Not mentioned | Full bug watcher with CLI |
+
+## Execution Checklist
+
+### 1. Memory Reconstruction
+- [x] Load latest checkpoint (ckpt-20260124-232253-c250be8e)
+- [x] STATUS sweep completed (65 directories, all complete)
+- [x] Create this tracking document
+- [x] Update after each major completion
+
+### 2. Documentation Updates
+
+#### 2.1 Root README.md
+- [x] **Quick Start** - Update with actual current commands
+- [x] **Architecture Diagram** - Replace with multi-agent pipeline view
+- [x] **Phase Status** - Update to Phase 12 COMPLETE
+- [x] **Component Table** - Add UI, observability, marketplace
+- [x] **CLI Reference** - Add `bugs`, pipeline orchestration commands
+- [x] **Integration Status** - Note external integrations deprecated
+- [x] **Production Constraints** - Add Vault token flow, consensus requirements
+- [x] **Cross-links** - Reference MULTI_AGENT_PIPELINE_ARCHITECTURE.md
+
+#### 2.2 Cross-Reference Updates
+- [x] Verify docs/ARCHITECTURE.md references are current
+- [x] Verify PHASE_DEPENDENCY_ANALYSIS.md alignment
+- [x] Verify STATUS_PROTOCOL.md is accurate
+
+### 3. Git Sync
+- [x] Identify missing commits (4 found)
+- [x] Push commits to origin (completed 2026-01-24)
+- [x] Commit README refresh (2026-01-24)
+
+### 4. Checkpoints
+
+| Stage | Checkpoint | Notes |
+|-------|------------|-------|
+| Start | ckpt-20260124-232253-c250be8e | Memory reconstructed |
+| README Draft | ckpt-20260124-234500-* | After README rewrite |
+| Final | ckpt-20260124-234500-* | All updates complete |
+
+---
+
+## Resume Instructions
+
+If this task is interrupted, resume with:
+
+```bash
+# 1. Load latest checkpoint
+checkpoint load
+
+# 2. Check this plan
+cat docs/README_REFRESH_PLAN.md
+
+# 3. Find incomplete items ([ ] markers)
+grep '\[ \]' docs/README_REFRESH_PLAN.md
+
+# 4. Continue from first incomplete item
+```
+
+---
+
+## Completed Items Log
+
+### 2026-01-24 23:45 UTC
+- Completed full README.md rewrite
+- Updated architecture diagram with multi-agent pipeline
+- Added all 12 phase status with test counts
+- Added CLI tools section (checkpoint, status, memory, bugs)
+- Added API endpoints documentation
+- Added production constraints (token revocation, consensus)
+- Cross-referenced all relevant docs
+- Committed and pushed to origin
+
+### 2026-01-24 23:30 UTC
+- Created README_REFRESH_PLAN.md
+- Analyzed gap between README and reality
+- Confirmed git sync complete (4 commits pushed)
+
+---
+
+*Documentation refresh COMPLETE. All items verified.*