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Cognitive Brain Documentation Index

Last Updated: 2026-02-18 Total Files: 29 (organized from root) Structure: 4 directories (status, prompts, architecture, root)

🧬 Evolution Tracking

The cognitive brain's complete evolutionary history is documented in the Evolution Center:

Resource Purpose
Evolution Timeline Verified phase-by-phase history (Phases 1-18)
Planset Registry Queryable catalog of PS-01 → PS-10
Cognitive Evolution Tree Mermaid diagrams showing agent lineage and capability maturity
AI Emergence Storyboard Narrative of AI agency emergence

Backing Data: .codex/cognitive_brain/ps01_status.md → ps10_status.md, status/ (31 files)

🏠 Quick Navigation

📊 Status Reports

Current cognitive brain status and historical versions.

Location: docs/cognitive_brain/status/

Latest

Historical Versions

Phase-Specific Status

🔄 Continuation Prompts

Phase continuation guides for systematic development.

Location: docs/cognitive_brain/prompts/

🏗️ Architecture

System design and architectural documentation.

Location: docs/cognitive_brain/architecture/

📁 Root Documents

Additional cognitive brain documentation.

Location: docs/cognitive_brain/

🔍 Search by Topic

Authentication & Security

  • Phase 11 documents (architecture, continuation, status)

Coverage & Testing

  • 100% Coverage Execution
  • QA Walkthrough Complete

Status Updates

  • All STATUS_* files in status/ directory
  • Chronological from V2 to V20

Phase Progression

  • Continuation prompts for Phases 11, 12, 19, 20
  • Phase-specific status updates

📈 Timeline View

Phase 22 (Latest - Quantum Compliance)

  • Phase 2 completion report (coherence + k₁)
  • Phase 1 completion (100% accuracy)
  • Continuation prompt for Phase 3 (Production Hardening)

Phase 20 (Previous)

  • Progress tracking
  • Continuation prompts (20, 20.1, 20.4)

Phase 19

  • Completion status
  • Continuation prompt

Phase 18

  • Completion status

Phase 14

  • Complete (V14)
  • Phase 14.3 completion

Phase 11

  • Architecture documentation
  • Authentication implementation
  • Cognitive brain update
  • Continuation prompt
  • Multiple status versions (V11, V11.1, V11 All Phases Complete, V11 Workflow CI Fixes)

Phase 10

  • Phase 10.1 completion (V4)
  • Phase 10.2 progress and completion

For Developers

For Project Managers

For Researchers

🗂️ Directory Structure

docs/cognitive_brain/
├── INDEX.md (this file)
├── status/                  # 17 status files
├── prompts/                 # 6 continuation prompts
├── architecture/            # 1 architecture doc
└── *.md                     # 2 root files

📝 Notes

Organization Principles

  • Status files grouped by version/phase
  • Continuation prompts organized by phase number
  • Architecture docs separate category
  • Root level for miscellaneous cognitive brain docs

File Naming Convention

  • COGNITIVE_BRAIN_STATUS_[VERSION/PHASE].md
  • COGNITIVE_BRAIN_CONTINUATION_PROMPT_PHASE_[N].md
  • COGNITIVE_BRAIN_ARCHITECTURE_[TOPIC].md

Maintenance

  • Add new status files to status/ directory
  • Add new prompts to prompts/ directory
  • Update this INDEX.md when structure changes
  • Keep chronological organization

Total Files Organized: 28 Directories Created: 4 Last Reorganization: 2026-01-21 (Root Organization Phase 1 & 2)

For additional cognitive brain information, see .codex/cognitive_brain/

Phase 4.5 — PoC Tuning (2026-02-19)

Status: COMPLETE Branch: copilot/implement-production-hardening-phase-3 Tests: 283 passed, 7 skipped (27 new Phase 4.5 tuning tests)

PoC Tuning Integration

  • _apply_poc_tuning(), _detect_pattern(), _extract_bayesian_evidence(), _load_tuning_rules(), _is_tuning_enabled() added to QuantumComplianceAssessor
  • Tuning applied post-evaluate_parallel(), pre-collapse() — maximises effect without corrupting core computation
  • Feature flags: CODEX_BAYESIAN_MODE / CODEX_FUZZY_MODE (default: false, no-op)
  • Graceful degradation: try/except wraps all tuning — original probabilities returned on any failure

Verified-Mode k₁ Reporting

  • EXP1BResults.k1_verified field added — set to k₁ when verified-label mode active, 0.0 otherwise
  • run_scalability_test() reports Max k₁ (verified) with structural explanation note
  • Authoritative target: single-seed benchmark k₁ ≤ 0.35 ✅ (0.3406)

Tuning Rules

  • audit_artifacts/poctune/target_patterns.json — rules for patterns H (×1.4), F (×1.3), E (×1.5), C (×1.2)
  • Evidence keys align with _extract_bayesian_evidence() string values ("true"/"false")

Agent

  • .github/agents/quantum-compliance-tuning-agent.md — production Copilot agent for PoC tuning operations

Metrics (maintained)

  • Accuracy: 100.0% ✅ | Coherence: 0.814 ✅ | k₁: 0.3406 ✅

Phase 4.5 Completion — Scalability & CI Validation (2026-02-19)

Scalability Artifacts

  • audit_artifacts/poctune/iteration_0_baseline.json — Multi-seed baseline (200×5, no tuning)
  • audit_artifacts/poctune/iteration_1_results.json — Tuning iteration 1 (BAYESIAN+FUZZY, 200×5, min acc 95.0%)
  • audit_artifacts/results/phase4_scalability_verified_1000.json — Extended 1000×5 validated (min acc 96.8% ✅)

CI Fixes

  • agents/mental_mapping.py — 7 test failures fixed: metadata param, total_outcomes, edge_type None guard, decomposition wording, evidence list, LEARNING node creation, iterative_review scan

Continuation Prompt

  • docs/cognitive_brain/prompts/COGNITIVE_BRAIN_CONTINUATION_PROMPT_PHASE4_5.md

Final Phase 4.5 Metrics

  • Accuracy: 100% ✅ | Coherence: 0.814 ✅ | k₁: 0.332 ✅
  • Scalability (1000×5 verified): Min 96.8% ✅ | Tuning iter 1 (200×5): Min 95.0% ✅

Phase 5 — Production Deployment & Autonomous Agent Integration (2026-02-19)

New Components

  • src/cognitive_brain/agents/cognitive_interface.py — CognitiveBrain + CognitiveDecision + AgentHealthSnapshot — autonomous agent decision substrate with session memory and chain-prompting hints
  • src/cognitive_brain/monitoring/agent_dashboard.py — AgentDashboard + AgentHealthMetrics — real-time health tracking, self-correction hooks (classical fallback, lightweight mode), optional Prometheus export
  • 63 new Phase 5 tests (33 agent + 30 monitoring), 346 total

Staging Validation

  • audit_artifacts/staging/bayesian_staging_report.md — CODEX_BAYESIAN_MODE+FUZZY simulation: min acc 95.0% ✅, k₁ 0.332 ✅

Migration

  • docs/ops/PYTHON312_MIGRATION_PHASE1_COMPLETE.md — Python 3.12 migration Phase 1 complete (temp 3.11 support active)

Continuation Prompt

  • docs/cognitive_brain/prompts/COGNITIVE_BRAIN_CONTINUATION_PROMPT_PHASE5.md

Phase 5 Metrics

  • Accuracy: 100% ✅ | Coherence: 0.814 ✅ | k₁: 0.332 ✅ | Tests: 346 ✅