Cognitive Evolution Tree — Process Mapping¶

%%{init: {'accessibility': {'title': 'Flowchart showing "🏛️ Foundation Era (2025-Q4)", Phase 1-5: Foundation<br/>Ingestion · Agents · RAG · CI/CD · Security'}}%%
graph TD
    subgraph Foundation["🏛️ Foundation Era (2025-Q4)"]
        P1[Phase 1-5: Foundation<br/>Ingestion · Agents · RAG · CI/CD · Security]
        P6[Phase 6: MCP Package System<br/>9 Topics · 93KB Docs]
    end

    subgraph Cognitive["🧠 Cognitive Era (2025-12 → 2026-01)"]
        P7[Phase 7: Cognitive Brain<br/>100+ Files · 22 Modules]
        P8[Phase 8: Doc Consolidation<br/>693+ Files Indexed]
        P9[Phase 9: Coverage & Perf<br/>90% Threshold · Hydra Training]
        P10[Phase 10: Genesis Foundation<br/>Owner Guard · Safety Layers]
    end

    subgraph Advancement["🚀 Advancement Era (2026-01 → Present)"]
        P11[Phase 11: MCP Advanced<br/>✅ PS-11 + PS-12 Complete]
        P12[Phase 12: Agent Enhancement<br/>✅ PS-13 Complete · 🟢 PS-14 Active]
        PS11[PS-11: Size Estimation ✅<br/>--estimate flag]
        PS12[PS-12: Exclude Patterns ✅<br/>--exclude flag]
        PS13[PS-13: Agent Task Router ✅<br/>L4 Classification · 7 Categories]
        PS14[PS-14: MSV Dashboard 🟢<br/>L3 Visualization · Design Complete]
        P11 --- PS11
        P11 --- PS12
        P12 --- PS13
        P12 --- PS14
    end

    subgraph Future["🔮 Future (2026-Q2+)"]
        P13[Phase 13: MCP Interactive]
        P14[Phase 14: Package Merge]
        P15[Phase 15: Agent Autonomy]
        P16[Phase 16: Self-Evolution]
        P17[Phase 17: Smart Recommendations]
        P18[Phase 18: Production Scaling]
    end

    P1 -->|"21,500+ tests"| P6
    P6 -->|"Package system"| P7
    P7 -->|"Brain online"| P8
    P8 -->|"Docs unified"| P9
    P9 -->|"Performance"| P10
    P10 -->|"Guards active"| P11
    P10 -->|"Guards active"| P12
    P11 -->|"Features"| P13
    P12 -->|"Coordination"| P15
    P13 -->|"Interactive"| P14
    P15 -->|"Autonomy"| P16
    P14 & P16 -->|"Intelligence"| P17
    P17 -->|"Scale"| P18

    style P1 fill:#2d5a27,color:#fff
    style P6 fill:#2d5a27,color:#fff
    style P7 fill:#2d5a27,color:#fff
    style P8 fill:#2d5a27,color:#fff
    style P9 fill:#2d5a27,color:#fff
    style P10 fill:#2d5a27,color:#fff
    style P11 fill:#2d5a27,color:#fff
    style P12 fill:#1a6b3c,color:#fff
    style PS11 fill:#2d5a27,color:#fff
    style PS12 fill:#2d5a27,color:#fff
    style PS13 fill:#2d5a27,color:#fff
    style PS14 fill:#1a6b3c,color:#fff
    style P13 fill:#b8860b,color:#fff
    style P14 fill:#b8860b,color:#fff
    style P15 fill:#b8860b,color:#fff
    style P16 fill:#b8860b,color:#fff
    style P17 fill:#b8860b,color:#fff
    style P18 fill:#b8860b,color:#fff

%%{init: {'accessibility': {'title': 'Flowchart showing "🔒 Security Plansets", PS-02: IPC Bridge<br/>Hardening'}}%%
graph LR
    subgraph Security["🔒 Security Plansets"]
        PS02[PS-02: IPC Bridge<br/>Hardening]
        PS04[PS-04: Privacy-First<br/>Memory PII]
        PS05[PS-05: Token Security<br/>Neutralization]
    end

    subgraph Architecture["🏗️ Architecture Plansets"]
        PS01[PS-01: Config<br/>Consolidation]
        PS03[PS-03: Split Brain<br/>Elimination]
        PS08[PS-08: Microservice<br/>Root Cleanup]
    end

    subgraph Intelligence["🧠 Intelligence Plansets"]
        PS06[PS-06: Knowledge<br/>Crawler]
        PS06e[PS-06e: Crawler<br/>Enhancement]
    end

    subgraph Operations["⚙️ Operations Plansets"]
        PS07[PS-07: Business Logic<br/>D365 SLA]
        PS09[PS-09: Training<br/>Unification]
        PS10[PS-10: Owner Guard<br/>CI/CD]
    end

    subgraph Advancement["🚀 Advancement Plansets"]
        PS11[PS-11: MCP Size<br/>Estimation ✅]
        PS12[PS-12: MCP Exclude<br/>Patterns ✅]
        PS13[PS-13: Agent Task<br/>Router ✅]
        PS14[PS-14: MSV Dashboard<br/>🟢 Active]
    end

    PS01 -->|"Config foundation"| PS03
    PS03 -->|"Unified state"| PS08
    PS02 -->|"Secure channels"| PS04
    PS04 -->|"PII clean"| PS05
    PS06 -->|"Base crawler"| PS06e
    PS07 -->|"Business rules"| PS09
    PS09 -->|"Training gates"| PS10
    PS05 -->|"Security baseline"| PS10
    PS08 -->|"Clean architecture"| PS10
    PS10 -->|"MCP features"| PS11
    PS10 -->|"MCP features"| PS12
    PS10 -->|"Agent routing"| PS13
    PS13 -->|"Visualization"| PS14

    style PS01 fill:#2d5a27,color:#fff
    style PS02 fill:#2d5a27,color:#fff
    style PS03 fill:#2d5a27,color:#fff
    style PS04 fill:#2d5a27,color:#fff
    style PS05 fill:#2d5a27,color:#fff
    style PS06 fill:#2d5a27,color:#fff
    style PS06e fill:#2d5a27,color:#fff
    style PS07 fill:#2d5a27,color:#fff
    style PS08 fill:#2d5a27,color:#fff
    style PS09 fill:#2d5a27,color:#fff
    style PS10 fill:#2d5a27,color:#fff
    style PS11 fill:#2d5a27,color:#fff
    style PS12 fill:#2d5a27,color:#fff
    style PS13 fill:#2d5a27,color:#fff
    style PS14 fill:#1a6b3c,color:#fff

%%{init: {'accessibility': {'title': 'Flowchart showing "Generation 1: Standalone Agents", CI Testing Agent'}}%%
graph TD
    subgraph Gen1["Generation 1: Standalone Agents"]
        A1[CI Testing Agent]
        A2[Bridge Security Monitor]
        A3[Config Validator]
    end

    subgraph Gen2["Generation 2: Coordinated Agents"]
        A4[Coverage Roadmap Agent]
        A5[Dependency Conflict Agent]
        A6[Test Alignment Fixer]
        A7[Documentation Quality Agent]
    end

    subgraph Gen3["Generation 3: Cognitive Agents"]
        A8[Cognitive Brain Manager]
        A9[Meta Tensor Validator]
        A10[RAG Index Manager]
        A11[QA Walkthrough Agent]
    end

    subgraph Gen4["Generation 4: Autonomous Agents"]
        A12[Repository Hygiene Agent]
        A13[Root Organizer Agent]
        A14[Workflow CI Fixer]
        A15[Session Analysis Agent]
    end

    subgraph Gen5["Generation 5: Self-Evolving (Future)"]
        A16[Self-Evolution Engine]
        A17[Multi-Agent Coordinator]
        A18[Adaptive Optimizer]
    end

    A1 -->|"Specialized"| A4
    A2 -->|"Security awareness"| A5
    A3 -->|"Config knowledge"| A6
    A4 -->|"Coverage patterns"| A8
    A5 -->|"Dependency graph"| A9
    A6 -->|"Test patterns"| A10
    A7 -->|"Doc standards"| A11
    A8 -->|"Brain integration"| A12
    A9 -->|"Tensor patterns"| A13
    A10 -->|"RAG knowledge"| A14
    A11 -->|"QA patterns"| A15
    A12 & A13 & A14 & A15 -->|"Evolution"| A16
    A16 -->|"Self-improve"| A17
    A17 -->|"Coordinate"| A18

    style A1 fill:#4a90d9,color:#fff
    style A2 fill:#4a90d9,color:#fff
    style A3 fill:#4a90d9,color:#fff
    style A4 fill:#2d7d46,color:#fff
    style A5 fill:#2d7d46,color:#fff
    style A6 fill:#2d7d46,color:#fff
    style A7 fill:#2d7d46,color:#fff
    style A8 fill:#8b5cf6,color:#fff
    style A9 fill:#8b5cf6,color:#fff
    style A10 fill:#8b5cf6,color:#fff
    style A11 fill:#8b5cf6,color:#fff
    style A12 fill:#dc6b2f,color:#fff
    style A13 fill:#dc6b2f,color:#fff
    style A14 fill:#dc6b2f,color:#fff
    style A15 fill:#dc6b2f,color:#fff
    style A16 fill:#b8860b,color:#fff
    style A17 fill:#b8860b,color:#fff
    style A18 fill:#b8860b,color:#fff

%%{init: {'accessibility': {'title': 'Flowchart showing "Level 1: Reactive", Code Suggestions'}}%%
graph LR
    subgraph L1["Level 1: Reactive"]
        L1a[Code Suggestions]
        L1b[Bug Detection]
    end

    subgraph L2["Level 2: Managed"]
        L2a[CI/CD Automation]
        L2b[Test Generation]
        L2c[Doc Updates]
    end

    subgraph L3["Level 3: Defined"]
        L3a[Agent Orchestration]
        L3b[Pattern Recognition]
        L3c[Knowledge Extraction]
    end

    subgraph L4["Level 4: Quantified ← Current"]
        L4a[Cognitive Brain]
        L4b[Self-Healing]
        L4c[Metrics-Driven]
    end

    subgraph L5["Level 5: Optimizing (Target)"]
        L5a[Self-Evolution]
        L5b[Autonomous Agency]
        L5c[Emergent Behavior]
    end

    L1 --> L2 --> L3 --> L4 --> L5

    style L1 fill:#666,color:#fff
    style L2 fill:#555,color:#fff
    style L3 fill:#444,color:#fff
    style L4 fill:#2d5a27,color:#fff
    style L5 fill:#b8860b,color:#fff

%%{init: {'accessibility': {'title': 'Timeline'}}%%
timeline
    title _codex_ Technology Evolution
    section Foundation (2025-Q4)
        Python Core : Ingestion pipeline
        PyTorch/ML : Model training infrastructure
        GitHub Actions : CI/CD workflows
    section Cognitive (2025-12 to 2026-01)
        Hydra Config : Unified configuration
        RAG Pipeline : Retrieval-augmented generation
        Cognitive Brain : Pattern detection and learning
        53 Copilot Agents : Specialized AI assistants
    section Advancement (2026-Q1)
        MCP Protocol : Model Context Protocol integration
        Knowledge Graphs : Structured memory
        Multi-Agent Coordination : Agent orchestration
    section Future (2026-Q2+)
        Self-Evolution : Adaptive optimization
        Autonomous Agency : Full AI autonomy
        Emergent Intelligence : Cross-agent learning