Cognitive Brain Documentation Index¶

Last Updated: 2026-05-08T08:34Z (S873) Total Files: 29+ (organized from root) Structure: 4 directories (status, prompts, architecture, root) Phase 9 (PR #4356): Autonomous Ops — 95% complete · S867–S873

🧬 Evolution Tracking¶

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

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

🏠 Quick Navigation¶

• Status Reports - Current state and version histories
• Continuation Prompts - Phase continuation guides
• Architecture - System design documents
• Root Documents - Miscellaneous cognitive brain files

📊 Status Reports¶

Current cognitive brain status and historical versions.

Location: docs/cognitive_brain/status/

Latest¶

• Phase 9 — Autonomous Ops 95% Complete — S867–S873 PR #4356 ⭐ CURRENT
• Phase 9 Deliverables — 15 completed, 4 pending post-merge
• CODEBASE_MERMAID_MAPS v1.2.0 — Sections 13-16 added (Autonomous Privilege, Rate-Limit, Session Handoff, Phase 9 Ops)
• Phase 4 Enhancement PoCs - Bayesian, Fuzzy Logic, Active Learning ✅
• Phase 3 Production Hardening - Quantum Compliance Phase 3 Complete ✅
• Phase 2 Completion Report - Quantum Compliance Phase 2 Complete ✅
• Phase 1 Completion (100%) - Accuracy 81.8% → 100%
• STATUS_V20_PROGRESS.md - Phase 20 progress
• STATUS_V19_COMPLETE.md - Phase 19 completion
• STATUS_V18_COMPLETE.md - Phase 18 completion

Historical Versions¶

• STATUS_V14_COMPLETE.md
• STATUS_V14_PHASE_14_3_COMPLETE.md
• STATUS_V11_ALL_PHASES_COMPLETE.md
• STATUS_V11_WORKFLOW_CI_FIXES.md
• STATUS_V11_1_CONTINUATION.md
• STATUS_V4_PHASE_10_1_COMPLETE.md
• STATUS_V3.md
• STATUS_V2.md

Phase-Specific Status¶

• STATUS_PHASE_10_2_COMPLETE.md
• STATUS_PHASE_10_2_PROGRESS.md
• STATUS_PHASE_UPDATE.md
• STATUS_PR_2858_UPDATE.md
• STATUS_QA_WALKTHROUGH_COMPLETE.md
• STATUS_UPDATE_2026_01_16.md
• STATUS_UPDATE_FINAL.md
• STATUS_SEARCH_RESULTS.md

🔄 Continuation Prompts¶

Phase continuation guides for systematic development.

Location: docs/cognitive_brain/prompts/

• CONTINUATION_PROMPT_PHASE_22.md - Phase 22 (Production Hardening)
• CONTINUATION_PROMPT_PHASE_20_4.md - Phase 20.4
• CONTINUATION_PROMPT_PHASE_20_1.md - Phase 20.1
• CONTINUATION_PROMPT_PHASE_20.md - Phase 20
• CONTINUATION_PROMPT_PHASE_19.md - Phase 19
• CONTINUATION_PROMPT_PHASE_12.md - Phase 12
• CONTINUATION_PROMPT_PHASE_11.md - Phase 11

🏗️ Architecture¶

System design and architectural documentation.

Location: docs/cognitive_brain/architecture/

• ARCHITECTURE_PHASE_11.md - Phase 11 architecture

📁 Root Documents¶

Additional cognitive brain documentation.

Location: docs/cognitive_brain/

• 100_PERCENT_COVERAGE_EXECUTION.md - Coverage execution report
• PHASE_11_1_COGNITIVE_BRAIN_UPDATE.md - Phase 11.1 update

🔍 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

🎯 Quick Links¶

For Developers¶

• Phase 2 Completion Report
• Phase 3 Continuation
• Latest Status
• Architecture

For Project Managers¶

• QA Walkthrough Status
• PR Updates
• Recent Updates (2026-01-16)

For Researchers¶

• Coverage Analysis
• Search Results

🗂️ 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 ✅