diff --git a/README.md b/README.md
index bc7e71b..09e7454 100644
--- a/README.md
+++ b/README.md
@@ -1,53 +1,232 @@
-# plingua
-The P-Lingua language for Membrane Computing
+# RR-PLingua: Relevance Realization Enhanced Membrane Computing
 
-P-Lingua is a comprehensive framework for membrane computing that provides a complete ecosystem for defining, parsing, simulating, and generating code for P-systems (membrane systems).
+**RR-PLingua** is an advanced membrane computing framework that integrates **Relevance Realization (RR)** dynamics with **OpenCog AtomSpace** symbolic reasoning, creating a unified platform for membrane computing with cognitive architectures.
 
-## 📚 Documentation
+## 🧠 RR-RNN: Relevance Realization with Recursive Neural Networks
+
+This implementation extends the traditional P-Lingua framework with four major Next Development Directions, creating a sophisticated system for symbolic-subsymbolic integration in membrane computing environments.
+
+### ✨ Key Features
+
+- **🔗 Advanced PLN Integration**: Probabilistic Logic Networks with RR pattern reasoning
+- **💬 Enhanced Scheme Interface**: Interactive REPL for system exploration and manipulation
+- **💾 Persistent AtomSpace**: JSON serialization and incremental learning capabilities
+- **🏗️ Multi-Level Integration**: Hierarchical membrane structures with cross-level emergence
+
+## 🎯 Implementation Summary
+
+### 1. Advanced PLN Integration ✅
+**File**: `include/pln_integration.hpp`
+
+- **PLN Truth Values**: Complete implementation with strength/confidence pairs
+- **Inference Rules**: 
+  - Deduction: A→B, A ⊢ B 
+  - Abduction: A→B, B ⊢ A (with reduced confidence)
+- **RR Pattern Implications**: Automatic generation of implications from high-coupling agent-arena relationships
+- **Full Inference Cycle**: Integrated PLN reasoning over membrane structures
 
-### [Comprehensive Architecture Documentation](docs/README.md)
-Detailed architectural insights with Mermaid diagrams covering:
-- **[System Architecture](docs/ARCHITECTURE.md)**: High-level design patterns and data flows
-- **[Component Deep Dive](docs/COMPONENTS.md)**: Internal architecture of parser, simulator, and generator
-- **[Usage Examples](docs/EXAMPLES.md)**: Practical demonstrations and integration guides
+### 2. Enhanced Scheme Interface ✅
+**File**: `include/scheme_interface.hpp`
 
-## Dependencies 
+- **Interactive REPL**: Full Scheme-style command evaluation
+- **Command Set**: 8+ commands for system exploration and manipulation
+- **Pattern Matching**: Query and analyze both RR and AtomSpace structures
+- **Real-time Updates**: Modify system state through Scheme commands
 
-* Linux OS (tested on Ubuntu 16.04 and Ubuntu 18.04)
-* GCC 4.9.0 or higher (with support for regex)
-* Flex
-* Bison
-* libboost-filesystem-dev 
-* libboost-program-options-dev
+### 3. Persistent AtomSpace ✅
+**File**: `include/persistent_atomspace.hpp`
 
-sudo apt-get install build-essential flex bison libboost-filesystem-dev libboost-program-options-dev 
+- **JSON Serialization**: Complete save/load for AtomSpace state
+- **RR Hypergraph Persistence**: Serialize all RR dynamics and structure
+- **Incremental Learning**: Merge new experiences with existing knowledge
+- **Memory Consolidation**: Remove low-confidence atoms to optimize storage
 
-## Compiling
+### 4. Multi-Level Integration ✅
+**Distributed across**: `relevance_realization.hpp`, `atomspace_integration.hpp`, test files
 
-* make grammar
-* make compiler
-* make simulator
-* sudo make install
+- **Hierarchical Structures**: Support for nested membrane architectures
+- **Cross-Level Emergence**: Detection of patterns spanning multiple hierarchy levels
+- **Temporal Reasoning**: Track relevance evolution over time
+- **Multi-Scale Dynamics**: Coordinated RR updates across system levels
 
-## Architecture Overview
+## 🏛️ Architecture Overview
 
 ```mermaid
 graph TD
-    A[P-Lingua Source] --> B[Parser]
-    B --> C[P-System Model]
-    C --> D[Simulator]
-    C --> E[Code Generator]
-    D --> F[Results]
-    E --> G[Generated Code]
+    subgraph "Traditional P-Lingua Core"
+        A[P-Lingua Source] --> B[Parser]
+        B --> C[P-System Model]
+        C --> D[Simulator]
+        C --> E[Code Generator]
+    end
     
-    style A fill:#e3f2fd
-    style C fill:#f3e5f5
-    style F fill:#e8f5e8
-    style G fill:#fff3e0
+    subgraph "RR Enhancement Layer"
+        F[RR Hypergraph] --> G[Relevance Dynamics]
+        G --> H[Agent-Arena-Relation Triad]
+        H --> I[Trialectic Co-constitution]
+    end
+    
+    subgraph "AtomSpace Integration"
+        J[OpenCog AtomSpace] --> K[PLN Inference]
+        K --> L[Pattern Recognition]
+        L --> M[Symbolic Reasoning]
+    end
+    
+    subgraph "Unified Architecture"
+        N[RR-AtomSpace Bridge]
+        O[Scheme Interface]
+        P[Persistent Storage]
+        Q[Multi-Level Coordination]
+    end
+    
+    C --> F
+    F --> J
+    J --> N
+    N --> O
+    N --> P
+    N --> Q
+    
+    style F fill:#e3f2fd
+    style J fill:#f3e5f5
+    style N fill:#e8f5e8
+    style O fill:#fff3e0
 ```
 
-The framework consists of three main components:
-- **Parser**: Transforms P-Lingua source into executable models
-- **Simulator**: Executes membrane computing simulations
-- **Generator**: Produces optimized C++ implementations
+## 🔄 RR Dynamics Process Flow
+
+```mermaid
+sequenceDiagram
+    participant Agent as Agent Membrane
+    participant Arena as Arena Membrane
+    participant RR as RR Engine
+    participant AtomSpace as AtomSpace
+    participant PLN as PLN Engine
+    
+    Agent->>RR: Update salience
+    Arena->>RR: Update affordances
+    RR->>RR: Compute trialectic dynamics
+    RR->>AtomSpace: Sync RR properties
+    AtomSpace->>PLN: Generate implications
+    PLN->>PLN: Perform inference cycle
+    PLN->>AtomSpace: Update truth values
+    AtomSpace->>RR: Feedback to RR dynamics
+    RR->>Agent: Update relevance gradient
+    RR->>Arena: Update coupling strength
+```
+
+## 🚀 Quick Start
+
+### Dependencies
+
+```bash
+sudo apt-get install build-essential flex bison libboost-filesystem-dev libboost-program-options-dev libfl-dev
+```
+
+### Build & Test
+
+```bash
+# Build traditional P-Lingua
+make grammar
+make compiler
+make simulator
+
+# Build RR-enhanced test programs
+g++ -I./include -std=c++11 -o test_rr_enhanced test_rr_enhanced.cpp
+g++ -I./include -std=c++11 -o test_next_directions test_next_directions.cpp
+g++ -I./include -std=c++11 -o demo_repl demo_repl.cpp
+
+# Run comprehensive demo
+./test_next_directions
+```
+
+### Interactive RR/AtomSpace REPL
+
+```bash
+./demo_repl
+```
+
+Available Scheme commands:
+```scheme
+(list-rr-nodes)           ; List all RR nodes with properties
+(list-atoms)              ; Show AtomSpace contents  
+(get-system-relevance)    ; Compute overall system relevance
+(run-pln-inference)       ; Execute PLN reasoning cycle
+(find-patterns)           ; Detect emergent patterns
+(get-salience node-ID)    ; Query node salience
+(update-salience node-ID VALUE) ; Modify node properties
+(find-atom "NAME")        ; Search atoms by name
+```
+
+## 📊 Performance Characteristics
+
+### RR Dynamics Complexity
+- **Trialectic Updates**: O(n) per node per timestep
+- **Coupling Computation**: O(n²) for agent-arena pairs
+- **Emergence Detection**: O(n·m) for n agents, m arenas
+
+### AtomSpace Integration
+- **RR→Atom Conversion**: O(n) for n RR nodes
+- **PLN Inference**: O(r·a) for r rules, a atoms
+- **Pattern Matching**: O(p·log(a)) for p patterns
+
+## 🔬 Research Applications
+
+### Cognitive Architecture Integration
+- **Symbolic-Subsymbolic Bridge**: RR provides the dynamic foundation for symbolic reasoning
+- **Emergent Pattern Recognition**: Multi-level emergence detection across membrane hierarchies
+- **Adaptive Learning**: Persistent storage enables incremental knowledge accumulation
+
+### Membrane Computing Enhancements
+- **Dynamic Rule Selection**: RR salience influences rule application priorities
+- **Adaptive Membrane Behavior**: Agent-arena coupling drives membrane evolution
+- **Hierarchical Organization**: Multi-level integration supports complex system architectures
+
+## 📚 Documentation
+
+### [Comprehensive RR-RNN Documentation](docs/README.md)
+Detailed technical documentation with diagrams covering:
+- **[RR-RNN Architecture](docs/ARCHITECTURE.md)**: Relevance Realization integration patterns
+- **[Component Deep Dive](docs/COMPONENTS.md)**: PLN, Scheme, and persistence systems
+- **[Usage Examples](docs/EXAMPLES.md)**: RR dynamics and AtomSpace integration demos
+
+### Core Implementation Files
+
+```
+include/
+├── relevance_realization.hpp    # RR framework with trialectic dynamics
+├── atomspace_integration.hpp    # RR-AtomSpace bridge
+├── pln_integration.hpp          # PLN inference engine
+├── scheme_interface.hpp         # Interactive Scheme REPL
+└── persistent_atomspace.hpp     # Serialization & persistence
+
+test_*.cpp                       # Comprehensive test suite
+demo_*.cpp                       # Interactive demonstrations
+```
+
+## 🎯 Future Extensions
+
+The implemented framework provides the foundation for:
+
+1. **Advanced Cognitive Architectures**: Full symbolic-subsymbolic integration
+2. **Distributed RR Systems**: Multi-agent relevance realization networks  
+3. **Learning Systems**: Persistent knowledge accumulation and refinement
+4. **Interactive Exploration**: Real-time system analysis and manipulation
+
+## 🤝 Contributing
+
+This RR-enhanced membrane computing framework represents a significant advancement toward unified cognitive architectures. Contributions are welcome in:
+
+- Enhanced RR dynamics algorithms
+- Additional PLN inference rules
+- Extended Scheme command sets
+- Multi-level emergence patterns
+- Performance optimizations
+
+## 📄 License
+
+Licensed under the same terms as the original P-Lingua framework.
+
+---
+
+*RR-PLingua successfully bridges dynamic self-organization (RR) and symbolic reasoning (AtomSpace/PLN), representing a significant advancement toward unified cognitive architectures.*
 
diff --git a/docs/ARCHITECTURE.md b/docs/ARCHITECTURE.md
index 5eaf44d..f1f556f 100644
--- a/docs/ARCHITECTURE.md
+++ b/docs/ARCHITECTURE.md
@@ -1,39 +1,71 @@
-# P-Lingua Architecture Documentation
+# RR-Enhanced P-Lingua Architecture Documentation
 
 ## Overview
 
-P-Lingua is a comprehensive framework for membrane computing that provides a complete ecosystem for defining, parsing, simulating, and generating code for P-systems (membrane systems). This documentation provides detailed architectural insights with visual diagrams to facilitate understanding and contribution.
+**RR-PLingua** is a revolutionary enhancement of the traditional P-Lingua framework that integrates **Relevance Realization (RR)** dynamics with **OpenCog AtomSpace** symbolic reasoning. This creates a sophisticated platform for cognitive membrane computing that bridges symbolic and subsymbolic processing.
+
+The enhanced system provides four major architectural innovations:
+1. **PLN Integration** - Probabilistic Logic Networks for uncertain reasoning
+2. **Scheme Interface** - Interactive exploration and manipulation
+3. **Persistent Storage** - Knowledge accumulation and memory consolidation  
+4. **Multi-Level Integration** - Hierarchical emergence detection
 
 ## High-Level System Architecture
 
 ```mermaid
 graph TD
-    A[P-Lingua Source Files] --> B[Lexical Analyzer]
-    B --> C[Parser]
-    C --> D[Syntax Tree]
-    D --> E[Semantic Analyzer]
-    E --> F[P-System Model]
-    F --> G[Simulator Engine]
-    F --> H[Code Generator]
-    G --> I[Configuration Output]
-    H --> J[C++ Generated Code]
-    
-    subgraph "Core Components"
-        K[Parser Module]
-        L[Simulator Module] 
-        M[Generator Module]
-        N[Serialization Module]
+    subgraph "Traditional P-Lingua Layer"
+        A[P-Lingua Source Files] --> B[Lexical Analyzer]
+        B --> C[Parser]
+        C --> D[Syntax Tree]
+        D --> E[Semantic Analyzer]
+        E --> F[P-System Model]
+        F --> G[Simulator Engine]
+        F --> H[Code Generator]
+        G --> I[Configuration Output]
+        H --> J[C++ Generated Code]
     end
     
-    C --> K
-    G --> L
-    H --> M
-    F --> N
+    subgraph "RR Enhancement Layer"
+        K[RR Hypergraph]
+        L[Trialectic Dynamics]
+        M[Agent-Arena-Relation]
+        N[Relevance Gradients]
+    end
     
-    style A fill:#e1f5fe
-    style F fill:#f3e5f5
-    style I fill:#e8f5e8
-    style J fill:#fff3e0
+    subgraph "AtomSpace Integration Layer"
+        O[OpenCog AtomSpace]
+        P[PLN Inference Engine]
+        Q[Truth Value Management]
+        R[Pattern Recognition]
+    end
+    
+    subgraph "Interactive & Persistence Layer"
+        S[Scheme REPL Interface]
+        T[JSON Serialization]
+        U[Memory Consolidation]
+        V[Multi-Level Coordination]
+    end
+    
+    F --> K
+    K --> L
+    L --> M
+    M --> N
+    
+    K --> O
+    O --> P
+    P --> Q
+    Q --> R
+    
+    O --> S
+    O --> T
+    T --> U
+    K --> V
+    
+    style K fill:#e3f2fd
+    style O fill:#f3e5f5
+    style S fill:#e8f5e8
+    style V fill:#fff3e0
 ```
 
 ## Core Data Structures
diff --git a/docs/COMPONENTS.md b/docs/COMPONENTS.md
index c298d3a..e33be94 100644
--- a/docs/COMPONENTS.md
+++ b/docs/COMPONENTS.md
@@ -1,6 +1,10 @@
-# P-Lingua Component Deep Dive
+# RR-Enhanced P-Lingua Component Deep Dive
 
-## Parser Component Architecture
+This document provides detailed analysis of both traditional P-Lingua components and the new RR-enhanced cognitive architecture components.
+
+## Traditional P-Lingua Components
+
+### Parser Component Architecture
 
 The parser component is the heart of P-Lingua's language processing pipeline, responsible for transforming P-Lingua source code into executable P-system models.
 
@@ -558,4 +562,264 @@ graph LR
     style I fill:#fff3e0
 ```
 
-This deep dive into P-Lingua's component architecture reveals the sophisticated design patterns and engineering decisions that make the framework both powerful and maintainable. Each component is designed with clear responsibilities and well-defined interfaces, enabling extensibility and optimization.
\ No newline at end of file
+This deep dive into P-Lingua's component architecture reveals the sophisticated design patterns and engineering decisions that make the framework both powerful and maintainable. Each component is designed with clear responsibilities and well-defined interfaces, enabling extensibility and optimization.
+
+## RR-Enhanced Components
+
+The RR enhancement layer adds four major component systems that transform traditional membrane computing into a cognitive architecture platform.
+
+### RR Hypergraph Component
+
+The RR Hypergraph is the core component that implements Relevance Realization dynamics through trialectic co-constitution.
+
+```mermaid
+classDiagram
+    class RRHypergraph {
+        +map~unsigned, RRNode~ nodes
+        +map~unsigned, RREdge~ edges
+        +set~unsigned~ agent_nodes
+        +set~unsigned~ arena_nodes
+        +set~unsigned~ relation_edges
+        +updateRelevanceRealization(delta_time)
+        +detectEmergentPatterns()
+        +computeCouplingStrength(agent_id, arena_id)
+        +addMembraneNode(membrane_id, label, aar_type)
+        +addRelationEdge(from, to, type, strength)
+    }
+    
+    class RRNode {
+        +unsigned id
+        +Type nodeType
+        +AARType aarType
+        +string label
+        +double salience
+        +double affordance_potential
+        +double affordance_realization
+        +vector~double~ trialectic_state
+        +computeRelevanceGradient()
+        +updateSalience(delta_time)
+        +computeTrialecticCoherence()
+    }
+    
+    class RREdge {
+        +unsigned id
+        +Type edgeType
+        +unsigned from_node
+        +unsigned to_node
+        +double strength
+        +double relevance_weight
+        +updateCoConstruction(from, to, delta_time)
+    }
+    
+    RRHypergraph --> RRNode
+    RRHypergraph --> RREdge
+```
+
+### AtomSpace Integration Component
+
+The AtomSpace Integration bridges RR dynamics with symbolic reasoning through OpenCog AtomSpace.
+
+```mermaid
+graph TB
+    subgraph "RR-AtomSpace Bridge"
+        A[RRAtomSpaceIntegrator]
+        B[Node Conversion]
+        C[Edge Conversion]
+        D[Property Synchronization]
+    end
+    
+    subgraph "AtomSpace Structure"
+        E[Concept Nodes]
+        F[Evaluation Links]
+        G[Inheritance Links]
+        H[Truth Values]
+    end
+    
+    subgraph "Pattern Detection"
+        I[Emergent Pattern Finder]
+        J[Coupling Analyzer]
+        K[Salience Tracker]
+    end
+    
+    A --> B
+    A --> C
+    A --> D
+    
+    B --> E
+    C --> F
+    D --> G
+    D --> H
+    
+    E --> I
+    F --> J
+    G --> K
+    
+    style A fill:#e8f5e8
+    style E fill:#f3e5f5
+    style I fill:#e3f2fd
+```
+
+### PLN Integration Component
+
+The PLN Integration component provides probabilistic logic reasoning over the integrated RR-AtomSpace structures.
+
+```mermaid
+flowchart TD
+    A[PLN Engine] --> B[Truth Value System]
+    A --> C[Inference Rules]
+    A --> D[Pattern Generator]
+    
+    B --> E[PLN Strength]
+    B --> F[PLN Confidence]
+    B --> G[Truth Operations]
+    
+    C --> H[Deduction Rule]
+    C --> I[Abduction Rule]
+    C --> J[Implication Generation]
+    
+    D --> K[RR Pattern Detector]
+    D --> L[Coupling Analyzer]
+    D --> M[Emergent Relation Creator]
+    
+    G --> H
+    G --> I
+    K --> J
+    L --> J
+    
+    style A fill:#e3f2fd
+    style B fill:#f3e5f5
+    style C fill:#e8f5e8
+    style D fill:#fff3e0
+```
+
+### Scheme Interface Component
+
+The Scheme Interface provides interactive exploration and manipulation capabilities.
+
+```mermaid
+graph LR
+    subgraph "REPL Interface"
+        A[Command Parser]
+        B[Expression Evaluator]
+        C[Result Formatter]
+    end
+    
+    subgraph "Command Categories"
+        D[RR Queries]
+        E[AtomSpace Queries]
+        F[System Updates]
+        G[Inference Control]
+    end
+    
+    subgraph "System Access"
+        H[RR Hypergraph Interface]
+        I[AtomSpace Interface]
+        J[PLN Engine Interface]
+    end
+    
+    A --> B
+    B --> C
+    
+    B --> D
+    B --> E
+    B --> F
+    B --> G
+    
+    D --> H
+    E --> I
+    F --> H
+    G --> J
+    
+    style B fill:#e8f5e8
+    style H fill:#f3e5f5
+```
+
+### Persistent Storage Component
+
+The Persistent Storage component handles serialization, memory consolidation, and incremental learning.
+
+```mermaid
+sequenceDiagram
+    participant PS as Persistent Storage
+    participant JSON as JSON Serializer
+    participant RR as RR Serializer
+    participant AS as AtomSpace Serializer
+    participant MC as Memory Consolidator
+    
+    PS->>RR: Serialize RR hypergraph
+    RR->>JSON: Convert to JSON format
+    JSON-->>PS: RR JSON data
+    
+    PS->>AS: Serialize AtomSpace
+    AS->>JSON: Convert to JSON format
+    JSON-->>PS: AtomSpace JSON data
+    
+    PS->>MC: Consolidate memory
+    MC->>MC: Remove low-confidence atoms
+    MC-->>PS: Optimized structures
+    
+    PS->>PS: Write to persistent storage
+```
+
+## Component Interaction Patterns
+
+### RR-AtomSpace Synchronization
+
+```mermaid
+sequenceDiagram
+    participant RR as RR Hypergraph
+    participant Bridge as Integration Bridge
+    participant AS as AtomSpace
+    participant PLN as PLN Engine
+    
+    RR->>Bridge: RR node updates
+    Bridge->>AS: Create/update concept nodes
+    AS->>Bridge: Confirm atom updates
+    Bridge->>RR: Sync confirmation
+    
+    RR->>Bridge: RR edge updates
+    Bridge->>AS: Create/update evaluation links
+    AS->>PLN: New relations available
+    PLN->>AS: Generate implications
+    AS->>Bridge: Pattern changes detected
+    Bridge->>RR: Feedback to RR dynamics
+```
+
+### Multi-Level Emergence Detection
+
+```mermaid
+graph TD
+    subgraph "Level Monitoring"
+        A[Agent Salience Monitor]
+        B[Arena Coupling Monitor]
+        C[Cross-Level Pattern Detector]
+    end
+    
+    subgraph "Emergence Criteria"
+        D[High Salience: > 0.8]
+        E[Strong Coupling: > 0.8]
+        F[High Coherence: > 0.6]
+    end
+    
+    subgraph "Emergence Actions"
+        G[Create Emergent Relation]
+        H[Update Multi-Level State]
+        I[Record Emergence Event]
+    end
+    
+    A --> D
+    B --> E
+    C --> F
+    
+    D --> G
+    E --> G
+    F --> G
+    
+    G --> H
+    H --> I
+    
+    style A fill:#e3f2fd
+    style G fill:#e8f5e8
+```
+
+This enhanced component architecture demonstrates how RR-PLingua successfully integrates dynamic self-organization with symbolic reasoning, creating a sophisticated platform for cognitive membrane computing applications.
\ No newline at end of file
diff --git a/docs/README.md b/docs/README.md
index 3bc826e..bd23f2f 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -1,8 +1,8 @@
-# P-Lingua Documentation Index
+# RR-PLingua Documentation Index
 
-## Welcome to P-Lingua Architecture Documentation
+## Welcome to RR-PLingua Architecture Documentation
 
-This comprehensive documentation suite provides detailed insights into the P-Lingua framework for membrane computing, featuring architectural diagrams, component analysis, and practical examples.
+This comprehensive documentation suite provides detailed insights into the **RR-PLingua** framework for enhanced membrane computing with **Relevance Realization (RR)** and **OpenCog AtomSpace** integration, featuring architectural diagrams, component analysis, and practical examples of cognitive membrane computing.
 
 ## Documentation Structure
 
@@ -12,6 +12,7 @@ graph TD
     A --> C[Component Deep Dive]
     A --> D[Usage Examples]
     A --> E[API Reference]
+    A --> RR[RR-RNN Integration]
     
     B --> F[System Architecture]
     B --> G[Data Flow Diagrams]
@@ -22,54 +23,86 @@ graph TD
     C --> K[Code Generator]
     C --> L[Serialization System]
     
+    RR --> PLN[PLN Integration]
+    RR --> SCHEME[Scheme Interface]
+    RR --> PERSIST[Persistent Storage]
+    RR --> MULTI[Multi-Level Systems]
+    
     D --> M[Basic Examples]
     D --> N[Advanced Patterns]
     D --> O[Integration Guides]
     D --> P[Performance Analysis]
+    D --> RRE[RR-Enhanced Examples]
     
     E --> Q[Parser API]
     E --> R[Simulator API]
     E --> S[Generator API]
     E --> T[Utility Functions]
+    E --> U[RR-AtomSpace API]
     
     style A fill:#e3f2fd
     style B fill:#f1f8e9
     style C fill:#fff3e0
     style D fill:#e8f5e8
     style E fill:#f3e5f5
+    style RR fill:#ffebee
 ```
 
 ## Quick Navigation
 
 ### 📐 [Architecture Overview](ARCHITECTURE.md)
-Comprehensive system-level view of P-Lingua's design patterns and architectural decisions.
+Comprehensive system-level view of RR-enhanced P-Lingua's design patterns and architectural decisions.
 
 **Key Diagrams:**
-- High-level system architecture
-- Core data structures
-- Module interaction patterns
-- Data flow and execution models
-- Memory management strategies
+- High-level RR-enhanced system architecture
+- Core RR data structures and AtomSpace integration
+- Module interaction patterns with cognitive components
+- Data flow and execution models for RR dynamics
+- Memory management strategies for persistent storage
 
 ### 🔧 [Component Deep Dive](COMPONENTS.md)
-Detailed analysis of individual components and their internal architectures.
+Detailed analysis of individual components and their internal architectures, including RR enhancements.
 
 **Covered Components:**
-- Parser component with lexical/semantic analysis
-- Simulator engine with rule selection algorithms
-- Code generator with template systems
-- Serialization framework with binary formats
+- Traditional P-Lingua: Parser, Simulator, Generator, Serialization
+- RR Hypergraph: Trialectic dynamics and relevance realization
+- AtomSpace Integration: Symbolic-subsymbolic bridge
+- PLN Engine: Probabilistic logic networks and inference
+- Scheme Interface: Interactive exploration and manipulation
+- Persistent Storage: Memory consolidation and incremental learning
 - Inter-component communication patterns
 
-### 💡 [Usage Examples](EXAMPLES.md)
-Practical demonstrations of P-Lingua features through working examples.
+### 🧠 [RR-RNN Architecture](RR_ARCHITECTURE.md)
+Comprehensive documentation of the Relevance Realization with Recursive Neural Networks enhancement.
+
+**RR-RNN Features:**
+- Trialectic co-constitution framework
+- Agent-Arena-Relation dynamics
+- PLN truth value systems and inference rules
+- Multi-level integration and emergence detection
+- Performance characteristics and computational complexity
+
+### 🔄 [RR Process Flows](RR_PROCESS_FLOWS.md)
+Detailed PlantUML diagrams showing RR-RNN system process flows.
+
+**Process Diagrams:**
+- Overall system process flow
+- RR trialectic dynamics process
+- PLN inference cycles
+- Scheme interface command processing
+- Persistent storage and memory consolidation
+- Multi-level emergence detection
+
+### 💡 [Usage Examples](RR_EXAMPLES.md)
+Practical demonstrations of RR-enhanced P-Lingua features through working examples.
 
 **Example Categories:**
-- Basic membrane systems
-- Complex division patterns
-- Pattern matching with variables
-- Multi-environment communication
-- Error handling scenarios
+- Basic RR-enhanced membrane systems
+- Advanced PLN integration patterns
+- Interactive Scheme interface usage
+- Persistent storage and memory consolidation
+- Multi-level integration with hierarchical structures
+- Complete RR-RNN system demonstrations
 
 ## Architecture Highlights
 
@@ -126,6 +159,30 @@ graph LR
 - Cross-platform support
 - Incremental loading
 
+#### 5. **RR Dynamics Pattern**
+- Trialectic co-constitution (∀^ω(x ⇔^α y ⇔^α z ⇔^α x))
+- Agent-arena-relation dynamics
+- Relevance gradient computation (∇ℜ = lim_{t→∞} Σᵢ log(aᵣᵢ(t)/aₚᵢ(t)))
+- Emergent pattern detection
+
+#### 6. **AtomSpace Integration Pattern**
+- RR-to-Atom conversion bridge
+- Truth value synchronization
+- PLN inference integration
+- Pattern matching and emergence detection
+
+#### 7. **Scheme Interface Pattern**
+- REPL command processing
+- Interactive system exploration
+- Real-time state manipulation
+- Lisp-style expression evaluation
+
+#### 8. **Persistent Storage Pattern**
+- JSON serialization framework
+- Memory consolidation algorithms
+- Incremental learning mechanisms
+- Cross-session knowledge persistence
+
 ## Component Interaction Map
 
 ```mermaid
diff --git a/docs/RR_ARCHITECTURE.md b/docs/RR_ARCHITECTURE.md
new file mode 100644
index 0000000..e4f273d
--- /dev/null
+++ b/docs/RR_ARCHITECTURE.md
@@ -0,0 +1,585 @@
+# RR-RNN Architecture Documentation
+
+## Overview
+
+The **RR-RNN (Relevance Realization with Recursive Neural Networks)** enhancement transforms traditional P-Lingua membrane computing into a sophisticated cognitive architecture platform by integrating:
+
+1. **Relevance Realization (RR) Dynamics** - Dynamic self-organization through agent-arena-relation triads
+2. **OpenCog AtomSpace Integration** - Symbolic knowledge representation and reasoning
+3. **PLN (Probabilistic Logic Networks)** - Inference over uncertain knowledge
+4. **Interactive Scheme Interface** - Real-time system exploration and manipulation
+
+## Core RR Architecture
+
+### Trialectic Co-Constitution Framework
+
+```mermaid
+graph TD
+    subgraph "Trialectic Dynamics"
+        A[Agent] --> |co-construction| B[Arena]
+        B --> |co-construction| C[Relation]
+        C --> |co-construction| A
+    end
+    
+    subgraph "RR Properties"
+        D[Salience]
+        E[Affordance Potential]
+        F[Affordance Realization]
+        G[Trialectic State Vector]
+    end
+    
+    subgraph "Mathematical Foundation"
+        H[∀^ω(x ⇔^α y ⇔^α z ⇔^α x)]
+        I[∇ℜ = lim_{t→∞} Σᵢ log(aᵣᵢ(t)/aₚᵢ(t))]
+        J[agent ↔^δ arena ∈ ℝ^(∞×∞)]
+    end
+    
+    A --> D
+    B --> E
+    C --> F
+    A --> G
+    
+    D --> H
+    E --> I
+    F --> J
+    
+    style A fill:#e3f2fd
+    style B fill:#f3e5f5
+    style C fill:#e8f5e8
+    style H fill:#fff3e0
+```
+
+### RR Hypergraph Structure
+
+```mermaid
+classDiagram
+    class RRNode {
+        +unsigned id
+        +Type nodeType
+        +AARType aarType
+        +string label
+        +double salience
+        +double affordance_potential
+        +double affordance_realization
+        +vector~double~ trialectic_state
+        +computeRelevanceGradient()
+        +updateSalience(delta_time)
+        +computeTrialecticCoherence()
+    }
+    
+    class RREdge {
+        +unsigned id
+        +Type edgeType
+        +unsigned from_node
+        +unsigned to_node
+        +double strength
+        +double relevance_weight
+        +updateCoConstruction(from, to, delta_time)
+    }
+    
+    class RRHypergraph {
+        +map~unsigned, RRNode~ nodes
+        +map~unsigned, RREdge~ edges
+        +set~unsigned~ agent_nodes
+        +set~unsigned~ arena_nodes
+        +set~unsigned~ relation_edges
+        +updateRelevanceRealization(delta_time)
+        +detectEmergentPatterns()
+        +computeCouplingStrength(agent_id, arena_id)
+    }
+    
+    class EmergentCluster {
+        +unsigned agent_id
+        +vector~unsigned~ arena_ids
+        +vector~double~ coupling_strengths
+        +double coherence
+    }
+    
+    RRHypergraph --> RRNode
+    RRHypergraph --> RREdge
+    RRHypergraph --> EmergentCluster
+    RRNode --> RREdge : connected by
+```
+
+## AtomSpace Integration Architecture
+
+### RR-AtomSpace Bridge
+
+```mermaid
+graph LR
+    subgraph "RR Hypergraph"
+        A[RR Nodes]
+        B[RR Edges]
+        C[RR Properties]
+    end
+    
+    subgraph "Bridge Layer"
+        D[RRAtomSpaceIntegrator]
+        E[Node Mapping]
+        F[Property Sync]
+        G[Pattern Detection]
+    end
+    
+    subgraph "OpenCog AtomSpace"
+        H[Concept Nodes]
+        I[Evaluation Links]
+        J[Inheritance Links]
+        K[Truth Values]
+    end
+    
+    A --> D
+    B --> D
+    C --> D
+    
+    D --> E
+    D --> F
+    D --> G
+    
+    E --> H
+    F --> K
+    G --> I
+    G --> J
+    
+    style D fill:#e8f5e8
+    style H fill:#f3e5f5
+```
+
+### Atom Structure Mapping
+
+```mermaid
+flowchart TD
+    subgraph "RR Node Transformation"
+        A[RR Node] --> B[Concept Node]
+        A --> C[Truth Value: salience, affordance]
+        A --> D[Inheritance: type, aar_type]
+    end
+    
+    subgraph "RR Edge Transformation"
+        E[RR Edge] --> F[Evaluation Link]
+        E --> G[Predicate: 'relates']
+        E --> H[Truth Value: strength, relevance]
+    end
+    
+    subgraph "AtomSpace Structure"
+        B --> I[Node Registry]
+        C --> I
+        D --> I
+        F --> J[Link Registry]
+        G --> J
+        H --> J
+    end
+    
+    I --> K[Pattern Matching]
+    J --> K
+    K --> L[Emergent Pattern Detection]
+    
+    style A fill:#e3f2fd
+    style B fill:#f3e5f5
+    style K fill:#e8f5e8
+```
+
+## PLN Integration Architecture
+
+### PLN Truth Value System
+
+```mermaid
+graph TB
+    subgraph "PLN Truth Values"
+        A[Strength Component]
+        B[Confidence Component]
+        C[PLNTruthValue = (s, c)]
+    end
+    
+    subgraph "PLN Operations"
+        D[Negation: NOT(A) = (1-s, c)]
+        E[Conjunction: AND(A,B) = (s_A * s_B, min(c_A, c_B))]
+        F[Disjunction: OR(A,B) = (s_A + s_B - s_A*s_B, min(c_A, c_B))]
+        G[Implication: A→B = (1-s_A+s_A*s_B, f(c_A,c_B))]
+    end
+    
+    subgraph "Inference Rules"
+        H[Deduction: A→B, A ⊢ B]
+        I[Abduction: A→B, B ⊢ A]
+        J[RR Pattern Implications]
+    end
+    
+    A --> C
+    B --> C
+    C --> D
+    C --> E
+    C --> F
+    C --> G
+    
+    D --> H
+    E --> I
+    F --> J
+    G --> J
+    
+    style C fill:#e3f2fd
+    style H fill:#f3e5f5
+    style J fill:#e8f5e8
+```
+
+### PLN Inference Cycle
+
+```mermaid
+sequenceDiagram
+    participant RR as RR Hypergraph
+    participant PLN as PLN Engine
+    participant AS as AtomSpace
+    participant Impl as Implications
+    
+    RR->>PLN: High-coupling patterns
+    PLN->>AS: Find agent-arena pairs
+    AS-->>PLN: Coupled nodes
+    PLN->>Impl: Generate implications
+    Impl->>AS: Create implication links
+    AS->>PLN: Start inference cycle
+    
+    loop Deduction
+        PLN->>AS: Find A→B, A patterns
+        AS-->>PLN: Matching patterns
+        PLN->>AS: Apply deduction: infer B
+    end
+    
+    loop Abduction
+        PLN->>AS: Find A→B, B patterns
+        AS-->>PLN: Matching patterns
+        PLN->>AS: Apply abduction: hypothesize A
+    end
+    
+    PLN-->>RR: Inference results
+    RR->>RR: Update RR dynamics
+```
+
+## Scheme Interface Architecture
+
+### REPL Command Processing
+
+```mermaid
+graph TD
+    subgraph "User Interface"
+        A[User Input]
+        B[Command Parser]
+        C[Expression Evaluator]
+    end
+    
+    subgraph "Command Types"
+        D[(list-rr-nodes)]
+        E[(list-atoms)]
+        F[(get-system-relevance)]
+        G[(run-pln-inference)]
+        H[(find-patterns)]
+        I[(get-salience node-ID)]
+        J[(update-salience node-ID VALUE)]
+        K[(find-atom "NAME")]
+    end
+    
+    subgraph "System Access"
+        L[RR Hypergraph Access]
+        M[AtomSpace Access]
+        N[PLN Engine Access]
+        O[Pattern Matcher]
+    end
+    
+    A --> B
+    B --> C
+    C --> D
+    C --> E
+    C --> F
+    C --> G
+    C --> H
+    C --> I
+    C --> J
+    C --> K
+    
+    D --> L
+    E --> M
+    F --> L
+    G --> N
+    H --> O
+    I --> L
+    J --> L
+    K --> M
+    
+    style C fill:#e8f5e8
+    style L fill:#f3e5f5
+```
+
+### Interactive Command Flow
+
+```mermaid
+stateDiagram-v2
+    [*] --> REPL_Start
+    REPL_Start --> Command_Input
+    Command_Input --> Parse_Expression
+    Parse_Expression --> Validate_Command
+    
+    Validate_Command --> Execute_Query: Read command
+    Validate_Command --> Execute_Update: Write command
+    Validate_Command --> Error_Handler: Invalid command
+    
+    Execute_Query --> Format_Response
+    Execute_Update --> Update_System
+    Update_System --> Format_Response
+    Error_Handler --> Format_Response
+    
+    Format_Response --> Command_Input
+    Command_Input --> [*]: quit/exit
+    
+    note right of Execute_Query
+        Commands like:
+        (list-rr-nodes)
+        (get-system-relevance)
+        (find-patterns)
+    end note
+    
+    note right of Execute_Update
+        Commands like:
+        (update-salience node-ID VALUE)
+        (run-pln-inference)
+    end note
+```
+
+## Persistent Storage Architecture
+
+### Serialization Framework
+
+```mermaid
+graph LR
+    subgraph "In-Memory Structures"
+        A[RR Hypergraph]
+        B[AtomSpace]
+        C[PLN State]
+    end
+    
+    subgraph "Serialization Layer"
+        D[JSON Serializer]
+        E[RR Serializer]
+        F[AtomSpace Serializer]
+        G[Consolidator]
+    end
+    
+    subgraph "Persistent Storage"
+        H[RR JSON File]
+        I[AtomSpace JSON File]
+        J[Merged Knowledge Base]
+    end
+    
+    A --> E
+    B --> F
+    C --> D
+    
+    E --> H
+    F --> I
+    D --> G
+    
+    G --> J
+    H --> J
+    I --> J
+    
+    style D fill:#e8f5e8
+    style J fill:#f3e5f5
+```
+
+### Memory Consolidation Process
+
+```mermaid
+flowchart TD
+    A[Current AtomSpace] --> B[Confidence Analysis]
+    B --> C{Confidence > Threshold?}
+    C -->|Yes| D[Keep Atom]
+    C -->|No| E[Mark for Removal]
+    
+    D --> F[Active Memory]
+    E --> G[Cleanup Queue]
+    
+    F --> H[Incremental Learning]
+    G --> I[Memory Optimization]
+    
+    H --> J[Merge New Experiences]
+    I --> K[Free Memory]
+    
+    J --> L[Updated Knowledge Base]
+    K --> L
+    
+    style B fill:#e3f2fd
+    style L fill:#e8f5e8
+```
+
+## Multi-Level Integration Architecture
+
+### Hierarchical Membrane Structure
+
+```mermaid
+graph TB
+    subgraph "Level 0: Environment"
+        A[Global Environment]
+    end
+    
+    subgraph "Level 1: Outer Membranes"
+        B[Outer Agent 1]
+        C[Outer Arena 1]
+        D[Outer Agent 2]
+        E[Outer Arena 2]
+    end
+    
+    subgraph "Level 2: Inner Membranes"
+        F[Inner Agent 1.1]
+        G[Inner Arena 1.1]
+        H[Inner Agent 1.2]
+        I[Inner Arena 1.2]
+    end
+    
+    subgraph "Cross-Level Dynamics"
+        J[Emergence Detection]
+        K[Coherence Propagation]
+        L[Temporal Reasoning]
+    end
+    
+    A --> B
+    A --> C
+    A --> D
+    A --> E
+    
+    B --> F
+    B --> G
+    C --> H
+    C --> I
+    
+    F --> J
+    G --> J
+    H --> K
+    I --> K
+    
+    J --> L
+    K --> L
+    
+    style A fill:#e3f2fd
+    style J fill:#e8f5e8
+```
+
+### Emergence Detection Algorithm
+
+```mermaid
+flowchart TD
+    A[Monitor Agent Salience] --> B{Salience > 0.8?}
+    B -->|Yes| C[Check Arena Coupling]
+    B -->|No| A
+    
+    C --> D{Coupling > 0.8?}
+    D -->|Yes| E[Measure Trialectic Coherence]
+    D -->|No| A
+    
+    E --> F{Coherence > 0.6?}
+    F -->|Yes| G[Detect Cross-Level Pattern]
+    F -->|No| A
+    
+    G --> H[Create Emergent Relation]
+    H --> I[Update Multi-Level State]
+    I --> J[Record Emergence Event]
+    J --> A
+    
+    style G fill:#e8f5e8
+    style H fill:#f3e5f5
+```
+
+## System Integration Flow
+
+### Complete RR-RNN Processing Pipeline
+
+```mermaid
+sequenceDiagram
+    participant User
+    participant Parser as P-Lingua Parser
+    participant RR as RR Engine
+    participant AS as AtomSpace
+    participant PLN as PLN Engine
+    participant Scheme as Scheme REPL
+    participant Storage as Persistent Storage
+    
+    User->>Parser: Load .pli file
+    Parser->>RR: Create RR hypergraph
+    RR->>AS: Initialize AtomSpace
+    AS->>PLN: Setup inference engine
+    
+    User->>Scheme: Start interactive session
+    
+    loop RR Dynamics
+        RR->>RR: Update trialectic states
+        RR->>AS: Sync node properties
+        AS->>PLN: Generate implications
+        PLN->>PLN: Perform inference cycle
+        PLN->>AS: Update truth values
+        AS->>RR: Feedback updates
+    end
+    
+    User->>Scheme: Execute commands
+    Scheme->>RR: Query/update RR state
+    Scheme->>AS: Query/update atoms
+    Scheme->>PLN: Trigger inference
+    Scheme-->>User: Return results
+    
+    User->>Storage: Save system state
+    Storage->>AS: Serialize AtomSpace
+    Storage->>RR: Serialize RR hypergraph
+    Storage-->>User: Confirm save
+```
+
+## Performance Characteristics
+
+### Computational Complexity Analysis
+
+```mermaid
+graph LR
+    subgraph "RR Operations"
+        A[Node Update: O(n)]
+        B[Edge Update: O(e)]
+        C[Emergence Detection: O(n²)]
+        D[Trialectic Dynamics: O(n)]
+    end
+    
+    subgraph "AtomSpace Operations"
+        E[Node Sync: O(n)]
+        F[Pattern Matching: O(a log a)]
+        G[Truth Value Update: O(a)]
+        H[Link Creation: O(l)]
+    end
+    
+    subgraph "PLN Operations"
+        I[Deduction: O(r·a)]
+        J[Abduction: O(r·a)]
+        K[Implication Generation: O(n²)]
+        L[Inference Cycle: O(r·a·c)]
+    end
+    
+    subgraph "Overall Complexity"
+        M[Per Step: O(n² + r·a·c)]
+        N[Memory: O(n + a + r)]
+        O[Storage: O(n + a)]
+    end
+    
+    A --> M
+    E --> M
+    I --> M
+    
+    A --> N
+    E --> N
+    
+    E --> O
+    A --> O
+    
+    style M fill:#ffebee
+    style N fill:#f3e5f5
+    style O fill:#e8f5e8
+```
+
+Where:
+- `n` = number of RR nodes
+- `e` = number of RR edges  
+- `a` = number of atoms
+- `r` = number of inference rules
+- `l` = number of links
+- `c` = inference cycles
+
+This architecture documentation provides a comprehensive view of how RR-RNN enhances traditional membrane computing with cognitive capabilities, creating a sophisticated platform for symbolic-subsymbolic integration and emergent pattern recognition.
\ No newline at end of file
diff --git a/docs/RR_EXAMPLES.md b/docs/RR_EXAMPLES.md
new file mode 100644
index 0000000..492451d
--- /dev/null
+++ b/docs/RR_EXAMPLES.md
@@ -0,0 +1,491 @@
+# RR-PLingua Usage Examples and Integration Guide
+
+This document provides comprehensive examples of using the RR-enhanced membrane computing framework, demonstrating all four major implementation areas with practical code examples and use cases.
+
+## Quick Start Example
+
+### Basic RR-Enhanced Membrane System
+
+```cpp
+#include <relevance_realization.hpp>
+#include <atomspace_integration.hpp>
+
+using namespace plingua::rr;
+using namespace plingua::atomspace;
+
+int main() {
+    // Create RR hypergraph
+    RRHypergraph hypergraph;
+    
+    // Add agent and arena membranes
+    unsigned agent = hypergraph.addMembraneNode(1, "cognitive_agent", AARType::AGENT);
+    unsigned arena = hypergraph.addMembraneNode(2, "task_environment", AARType::ARENA);
+    
+    // Create co-construction relation
+    hypergraph.addRelationEdge(agent, arena, RREdge::CO_CONSTRUCTION, 0.7);
+    
+    // Setup AtomSpace integration
+    AtomSpace atomspace;
+    RRAtomSpaceIntegrator integrator(&hypergraph, &atomspace);
+    
+    // Run RR dynamics for 10 steps
+    for (int i = 0; i < 10; ++i) {
+        hypergraph.updateRelevanceRealization(0.1);
+        integrator.performIntegration();
+    }
+    
+    // Find emergent patterns
+    auto patterns = integrator.findEmergentPatterns();
+    for (const auto& pattern : patterns) {
+        std::cout << "Detected: " << pattern << std::endl;
+    }
+    
+    return 0;
+}
+```
+
+## Advanced PLN Integration Examples
+
+### 1. PLN Truth Value Operations
+
+```cpp
+#include <pln_integration.hpp>
+
+using namespace plingua::pln;
+
+void demonstratePLNOperations() {
+    // Create PLN truth values
+    PLNTruthValue agent_belief(0.8, 0.9);      // High strength, high confidence
+    PLNTruthValue arena_state(0.6, 0.7);      // Medium strength, good confidence
+    
+    // Perform PLN operations
+    auto conjunction = agent_belief.conjunction(arena_state);
+    std::cout << "Conjunction: strength=" << conjunction.strength 
+              << ", confidence=" << conjunction.confidence << std::endl;
+    
+    auto implication = agent_belief.implication(arena_state);
+    std::cout << "Implication: strength=" << implication.strength 
+              << ", confidence=" << implication.confidence << std::endl;
+    
+    auto negation = agent_belief.negate();
+    std::cout << "Negation: strength=" << negation.strength 
+              << ", confidence=" << negation.confidence << std::endl;
+}
+```
+
+### 2. PLN Inference Engine Usage
+
+```cpp
+void demonstratePLNInference() {
+    RRHypergraph hypergraph;
+    AtomSpace atomspace;
+    PLNInferenceEngine pln_engine(&atomspace);
+    
+    // Create high-coupling agent-arena pair
+    unsigned agent = hypergraph.addMembraneNode(1, "learning_agent", AARType::AGENT);
+    unsigned arena = hypergraph.addMembraneNode(2, "learning_environment", AARType::ARENA);
+    hypergraph.addRelationEdge(agent, arena, RREdge::CO_CONSTRUCTION, 0.85);
+    
+    // Integrate with AtomSpace
+    RRAtomSpaceIntegrator integrator(&hypergraph, &atomspace);
+    integrator.performIntegration();
+    
+    // Generate RR-based implications
+    pln_engine.generateRRImplications(&hypergraph);
+    
+    // Perform deduction
+    auto deductions = pln_engine.performDeduction();
+    std::cout << "Generated " << deductions.size() << " new deductions" << std::endl;
+    
+    // Perform abduction (hypothesis generation)
+    auto abductions = pln_engine.performAbduction();
+    std::cout << "Generated " << abductions.size() << " new hypotheses" << std::endl;
+    
+    // Full inference cycle
+    pln_engine.performInferenceCycle(&hypergraph);
+    auto results = pln_engine.getInferenceResults();
+    
+    for (const auto& result : results) {
+        std::cout << "PLN Result: " << result << std::endl;
+    }
+}
+```
+
+## Scheme Interface Examples
+
+### 1. Interactive REPL Session
+
+```cpp
+#include <scheme_interface.hpp>
+
+using namespace plingua::scheme;
+
+void interactiveSchemeSession() {
+    RRHypergraph hypergraph;
+    AtomSpace atomspace;
+    
+    // Setup test environment
+    unsigned agent = hypergraph.addMembraneNode(1, "interactive_agent", AARType::AGENT);
+    unsigned arena = hypergraph.addMembraneNode(2, "interactive_arena", AARType::ARENA);
+    hypergraph.addRelationEdge(agent, arena, RREdge::INTERACTION, 0.75);
+    
+    // Setup AtomSpace integration
+    RRAtomSpaceIntegrator integrator(&hypergraph, &atomspace);
+    integrator.performIntegration();
+    
+    // Create Scheme evaluator
+    SchemeEvaluator evaluator(&hypergraph, &atomspace);
+    
+    // Start interactive REPL
+    std::cout << "Starting Scheme REPL..." << std::endl;
+    evaluator.startREPL();  // This will run interactively
+}
+```
+
+### 2. Programmatic Scheme Commands
+
+```cpp
+void programmaticSchemeCommands() {
+    RRHypergraph hypergraph;
+    AtomSpace atomspace;
+    SchemeEvaluator evaluator(&hypergraph, &atomspace);
+    
+    // Execute various Scheme commands programmatically
+    std::vector<std::string> commands = {
+        "(list-rr-nodes)",
+        "(get-system-relevance)",
+        "(find-patterns)",
+        "(get-salience node-1)",
+        "(update-salience node-1 0.9)",
+        "(run-pln-inference)",
+        "(find-atom \"agent\")"
+    };
+    
+    for (const auto& cmd : commands) {
+        std::string result = evaluator.evaluate(cmd);
+        std::cout << "Command: " << cmd << std::endl;
+        std::cout << "Result: " << result << std::endl << std::endl;
+    }
+}
+```
+
+## Persistent Storage Examples
+
+### 1. Basic Save and Load Operations
+
+```cpp
+#include <persistent_atomspace.hpp>
+
+using namespace plingua::persistent;
+
+void demonstratePersistence() {
+    RRHypergraph hypergraph;
+    AtomSpace atomspace;
+    PersistentAtomSpace storage;
+    
+    // Create and populate system
+    unsigned agent = hypergraph.addMembraneNode(1, "persistent_agent", AARType::AGENT);
+    unsigned arena = hypergraph.addMembraneNode(2, "persistent_arena", AARType::ARENA);
+    hypergraph.addRelationEdge(agent, arena, RREdge::CO_CONSTRUCTION, 0.8);
+    
+    RRAtomSpaceIntegrator integrator(&hypergraph, &atomspace);
+    integrator.performIntegration();
+    
+    // Save to files
+    bool atomspace_saved = storage.saveToFile(&atomspace, "system_atomspace.json");
+    bool rr_saved = storage.saveRRHypergraph(&hypergraph, "system_rr_hypergraph.json");
+    
+    std::cout << "AtomSpace saved: " << (atomspace_saved ? "Success" : "Failed") << std::endl;
+    std::cout << "RR Hypergraph saved: " << (rr_saved ? "Success" : "Failed") << std::endl;
+    
+    // Load from files
+    AtomSpace loaded_atomspace;
+    RRHypergraph loaded_hypergraph;
+    
+    bool atomspace_loaded = storage.loadFromFile(&loaded_atomspace, "system_atomspace.json");
+    bool rr_loaded = storage.loadRRHypergraph(&loaded_hypergraph, "system_rr_hypergraph.json");
+    
+    std::cout << "AtomSpace loaded: " << (atomspace_loaded ? "Success" : "Failed") << std::endl;
+    std::cout << "RR Hypergraph loaded: " << (rr_loaded ? "Success" : "Failed") << std::endl;
+}
+```
+
+### 2. Memory Consolidation and Incremental Learning
+
+```cpp
+void demonstrateMemoryConsolidation() {
+    AtomSpace atomspace;
+    PersistentAtomSpace storage;
+    
+    // Create atoms with varying confidence levels
+    unsigned high_conf_atom = atomspace.addConceptNode("reliable_knowledge", 0.9, 0.95);
+    unsigned med_conf_atom = atomspace.addConceptNode("uncertain_knowledge", 0.6, 0.4);
+    unsigned low_conf_atom = atomspace.addConceptNode("unreliable_knowledge", 0.3, 0.1);
+    
+    std::cout << "Before consolidation: " << atomspace.atoms.size() << " atoms" << std::endl;
+    
+    // Consolidate memory (remove atoms with confidence < 0.3)
+    storage.consolidateMemory(&atomspace, 0.3);
+    
+    std::cout << "After consolidation: " << atomspace.atoms.size() << " atoms" << std::endl;
+    
+    // Demonstrate incremental learning
+    AtomSpace new_experience;
+    unsigned new_atom = new_experience.addConceptNode("new_knowledge", 0.8, 0.85);
+    
+    // Merge new experience with existing knowledge
+    storage.mergeAtomSpaces(&atomspace, &new_experience);
+    
+    std::cout << "After merging new experience: " << atomspace.atoms.size() << " atoms" << std::endl;
+}
+```
+
+## Multi-Level Integration Examples
+
+### 1. Hierarchical Membrane Structure
+
+```cpp
+void demonstrateHierarchicalStructure() {
+    RRHypergraph hypergraph;
+    
+    // Create hierarchical structure
+    unsigned environment = hypergraph.addMembraneNode(0, "global_environment", AARType::ARENA);
+    
+    // Level 1: Outer membranes
+    unsigned outer_agent = hypergraph.addMembraneNode(1, "outer_cognitive_system", AARType::AGENT);
+    unsigned outer_arena = hypergraph.addMembraneNode(2, "outer_task_domain", AARType::ARENA);
+    
+    // Level 2: Inner membranes
+    unsigned inner_agent1 = hypergraph.addMembraneNode(3, "perception_module", AARType::AGENT);
+    unsigned inner_agent2 = hypergraph.addMembraneNode(4, "action_module", AARType::AGENT);
+    unsigned inner_arena1 = hypergraph.addMembraneNode(5, "sensory_space", AARType::ARENA);
+    unsigned inner_arena2 = hypergraph.addMembraneNode(6, "motor_space", AARType::ARENA);
+    
+    // Create hierarchical relations
+    hypergraph.addRelationEdge(environment, outer_agent, RREdge::CO_CONSTRUCTION, 0.6);
+    hypergraph.addRelationEdge(environment, outer_arena, RREdge::CO_CONSTRUCTION, 0.6);
+    hypergraph.addRelationEdge(outer_agent, outer_arena, RREdge::INTERACTION, 0.8);
+    
+    hypergraph.addRelationEdge(outer_agent, inner_agent1, RREdge::CO_CONSTRUCTION, 0.7);
+    hypergraph.addRelationEdge(outer_agent, inner_agent2, RREdge::CO_CONSTRUCTION, 0.7);
+    hypergraph.addRelationEdge(outer_arena, inner_arena1, RREdge::CO_CONSTRUCTION, 0.7);
+    hypergraph.addRelationEdge(outer_arena, inner_arena2, RREdge::CO_CONSTRUCTION, 0.7);
+    
+    hypergraph.addRelationEdge(inner_agent1, inner_arena1, RREdge::INTERACTION, 0.9);
+    hypergraph.addRelationEdge(inner_agent2, inner_arena2, RREdge::INTERACTION, 0.9);
+    
+    std::cout << "Created hierarchical structure with " << hypergraph.nodes.size() << " nodes" << std::endl;
+    std::cout << "and " << hypergraph.edges.size() << " edges" << std::endl;
+    
+    // Run multi-level dynamics
+    for (int i = 0; i < 20; ++i) {
+        hypergraph.updateRelevanceRealization(0.05);
+    }
+    
+    // Analyze cross-level emergence
+    double outer_salience = hypergraph.nodes[outer_agent]->salience;
+    double inner_coherence = (hypergraph.nodes[inner_agent1]->computeTrialecticCoherence() + 
+                             hypergraph.nodes[inner_agent2]->computeTrialecticCoherence()) / 2.0;
+    
+    if (outer_salience > 0.6 && inner_coherence > 0.3) {
+        std::cout << "Cross-level emergence detected!" << std::endl;
+        std::cout << "Outer salience: " << outer_salience << std::endl;
+        std::cout << "Inner coherence: " << inner_coherence << std::endl;
+    }
+}
+```
+
+### 2. Temporal Reasoning and Evolution Tracking
+
+```cpp
+void demonstrateTemporalReasoning() {
+    RRHypergraph hypergraph;
+    
+    // Create simple agent-arena system
+    unsigned agent = hypergraph.addMembraneNode(1, "evolving_agent", AARType::AGENT);
+    unsigned arena = hypergraph.addMembraneNode(2, "changing_arena", AARType::ARENA);
+    hypergraph.addRelationEdge(agent, arena, RREdge::CO_CONSTRUCTION, 0.5);
+    
+    // Track system evolution over time
+    std::vector<double> temporal_relevance;
+    std::vector<double> temporal_coupling;
+    
+    for (int t = 0; t < 50; ++t) {
+        hypergraph.updateRelevanceRealization(0.1);
+        
+        // Calculate system-wide relevance
+        double total_relevance = 0.0;
+        for (auto it = hypergraph.nodes.begin(); it != hypergraph.nodes.end(); ++it) {
+            total_relevance += it->second->computeRelevanceGradient();
+        }
+        double avg_relevance = total_relevance / hypergraph.nodes.size();
+        temporal_relevance.push_back(avg_relevance);
+        
+        // Calculate coupling strength
+        double coupling = hypergraph.computeCouplingStrength(agent, arena);
+        temporal_coupling.push_back(coupling);
+        
+        if (t % 10 == 0) {
+            std::cout << "Time " << t << ": relevance=" << avg_relevance 
+                      << ", coupling=" << coupling << std::endl;
+        }
+    }
+    
+    // Analyze temporal trends
+    if (temporal_relevance.size() >= 10) {
+        double recent_avg = 0.0, earlier_avg = 0.0;
+        for (int i = 0; i < 10; ++i) {
+            recent_avg += temporal_relevance[temporal_relevance.size() - 1 - i];
+            earlier_avg += temporal_relevance[i];
+        }
+        recent_avg /= 10;
+        earlier_avg /= 10;
+        
+        double trend = recent_avg - earlier_avg;
+        std::cout << "Temporal trend: " << (trend > 0.01 ? "increasing" : 
+                                          trend < -0.01 ? "decreasing" : "stable") 
+                  << " (Δ=" << trend << ")" << std::endl;
+    }
+}
+```
+
+## Complete Integration Example
+
+### Full RR-RNN System Demonstration
+
+```cpp
+#include <relevance_realization.hpp>
+#include <atomspace_integration.hpp>
+#include <pln_integration.hpp>
+#include <scheme_interface.hpp>
+#include <persistent_atomspace.hpp>
+
+void fullSystemDemo() {
+    std::cout << "=== Full RR-RNN System Demonstration ===" << std::endl;
+    
+    // Initialize all components
+    RRHypergraph hypergraph;
+    AtomSpace atomspace;
+    RRAtomSpaceIntegrator integrator(&hypergraph, &atomspace);
+    PLNInferenceEngine pln_engine(&atomspace);
+    SchemeEvaluator scheme_eval(&hypergraph, &atomspace);
+    PersistentAtomSpace storage;
+    
+    // Create test environment
+    unsigned env = hypergraph.addMembraneNode(0, "test_environment", AARType::ARENA);
+    unsigned agent = hypergraph.addMembraneNode(1, "cognitive_agent", AARType::AGENT);
+    unsigned arena = hypergraph.addMembraneNode(2, "task_arena", AARType::ARENA);
+    
+    hypergraph.addRelationEdge(env, agent, RREdge::INTERACTION, 0.5);
+    hypergraph.addRelationEdge(agent, arena, RREdge::CO_CONSTRUCTION, 0.7);
+    
+    // Phase 1: RR Dynamics Evolution
+    std::cout << "\n--- Phase 1: RR Dynamics ---" << std::endl;
+    for (int i = 0; i < 15; ++i) {
+        hypergraph.updateRelevanceRealization(0.1);
+        if (i % 5 == 0) {
+            integrator.performIntegration();
+            auto patterns = integrator.findEmergentPatterns();
+            if (!patterns.empty()) {
+                std::cout << "Step " << i << " - Emergent patterns: " << patterns.size() << std::endl;
+            }
+        }
+    }
+    
+    // Phase 2: PLN Integration
+    std::cout << "\n--- Phase 2: PLN Integration ---" << std::endl;
+    pln_engine.generateRRImplications(&hypergraph);
+    pln_engine.performInferenceCycle(&hypergraph);
+    auto pln_results = pln_engine.getInferenceResults();
+    
+    for (const auto& result : pln_results) {
+        std::cout << "PLN: " << result << std::endl;
+    }
+    
+    // Phase 3: Scheme Interface
+    std::cout << "\n--- Phase 3: Scheme Interface ---" << std::endl;
+    std::vector<std::string> demo_commands = {
+        "(get-system-relevance)",
+        "(find-patterns)",
+        "(run-pln-inference)",
+        "(list-rr-nodes)"
+    };
+    
+    for (const auto& cmd : demo_commands) {
+        std::string result = scheme_eval.evaluate(cmd);
+        std::cout << "scheme> " << cmd << std::endl;
+        std::cout << result << std::endl;
+    }
+    
+    // Phase 4: Persistence
+    std::cout << "\n--- Phase 4: Persistence ---" << std::endl;
+    bool atomspace_saved = storage.saveToFile(&atomspace, "/tmp/full_demo_atomspace.json");
+    bool rr_saved = storage.saveRRHypergraph(&hypergraph, "/tmp/full_demo_rr.json");
+    
+    std::cout << "System state saved: " 
+              << (atomspace_saved && rr_saved ? "Success" : "Failed") << std::endl;
+    
+    // Memory consolidation
+    size_t atoms_before = atomspace.atoms.size();
+    storage.consolidateMemory(&atomspace, 0.3);
+    size_t atoms_after = atomspace.atoms.size();
+    
+    std::cout << "Memory consolidation: " << atoms_before << " → " << atoms_after 
+              << " atoms (removed " << (atoms_before - atoms_after) << ")" << std::endl;
+    
+    std::cout << "\n=== Full System Demo Complete ===" << std::endl;
+}
+```
+
+## Performance Monitoring Examples
+
+### System Performance Analysis
+
+```cpp
+void performanceAnalysis() {
+    RRHypergraph hypergraph;
+    AtomSpace atomspace;
+    
+    // Create larger test system
+    const int num_agents = 10;
+    const int num_arenas = 8;
+    
+    std::vector<unsigned> agents, arenas;
+    
+    for (int i = 0; i < num_agents; ++i) {
+        agents.push_back(hypergraph.addMembraneNode(i, "agent_" + std::to_string(i), AARType::AGENT));
+    }
+    
+    for (int i = 0; i < num_arenas; ++i) {
+        arenas.push_back(hypergraph.addMembraneNode(100 + i, "arena_" + std::to_string(i), AARType::ARENA));
+    }
+    
+    // Create connections
+    for (unsigned agent : agents) {
+        for (unsigned arena : arenas) {
+            if (rand() % 100 < 30) { // 30% connection probability
+                double strength = 0.3 + (rand() % 50) / 100.0;
+                hypergraph.addRelationEdge(agent, arena, RREdge::INTERACTION, strength);
+            }
+        }
+    }
+    
+    std::cout << "Created system with " << hypergraph.nodes.size() << " nodes and " 
+              << hypergraph.edges.size() << " edges" << std::endl;
+    
+    // Performance timing
+    auto start_time = std::chrono::high_resolution_clock::now();
+    
+    for (int i = 0; i < 100; ++i) {
+        hypergraph.updateRelevanceRealization(0.05);
+    }
+    
+    auto end_time = std::chrono::high_resolution_clock::now();
+    auto duration = std::chrono::duration_cast<std::chrono::milliseconds>(end_time - start_time);
+    
+    std::cout << "100 RR update cycles completed in " << duration.count() << " ms" << std::endl;
+    std::cout << "Average per cycle: " << (duration.count() / 100.0) << " ms" << std::endl;
+}
+```
+
+These comprehensive examples demonstrate the full capabilities of the RR-enhanced membrane computing framework, showing how to leverage all four major implementation areas for sophisticated cognitive architecture applications.
\ No newline at end of file
diff --git a/docs/RR_PROCESS_FLOWS.md b/docs/RR_PROCESS_FLOWS.md
new file mode 100644
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+++ b/docs/RR_PROCESS_FLOWS.md
@@ -0,0 +1,518 @@
+# RR-RNN Process Flow Diagrams
+
+This document contains PlantUML diagrams showing the detailed process flows of the RR-RNN system components.
+
+## Overall System Process Flow
+
+```plantuml
+@startuml RR-RNN-System-Flow
+!theme plain
+title RR-RNN System Process Flow
+
+actor User
+participant "P-Lingua Parser" as Parser
+participant "RR Hypergraph" as RR
+participant "AtomSpace" as AS
+participant "PLN Engine" as PLN
+participant "Scheme REPL" as Scheme
+participant "Persistent Storage" as Storage
+
+== Initialization ==
+User -> Parser: Load P-system definition
+Parser -> RR: Create RR hypergraph from membranes
+RR -> AS: Initialize AtomSpace integration
+AS -> PLN: Setup PLN inference engine
+PLN -> Scheme: Register command interface
+
+== Runtime Dynamics ==
+loop Continuous RR Evolution
+    RR -> RR: Update trialectic states
+    note right: ∀^ω(x ⇔^α y ⇔^α z ⇔^α x)
+    
+    RR -> RR: Compute relevance gradients
+    note right: ∇ℜ = lim_{t→∞} Σᵢ log(aᵣᵢ(t)/aₚᵢ(t))
+    
+    RR -> AS: Synchronize node properties
+    AS -> PLN: Generate new implications
+    
+    PLN -> PLN: Perform deduction cycle
+    note right: A→B, A ⊢ B
+    
+    PLN -> PLN: Perform abduction cycle  
+    note right: A→B, B ⊢ A (reduced confidence)
+    
+    PLN -> AS: Update truth values
+    AS -> RR: Feedback relevance updates
+    
+    RR -> RR: Detect emergent patterns
+    note right: Agent-arena coupling > threshold
+end
+
+== Interactive Exploration ==
+User -> Scheme: Execute Scheme commands
+alt Query Commands
+    Scheme -> RR: (list-rr-nodes)
+    RR -> Scheme: Return node properties
+else Update Commands  
+    Scheme -> RR: (update-salience node-ID value)
+    RR -> AS: Propagate changes
+    AS -> PLN: Trigger inference update
+else Inference Commands
+    Scheme -> PLN: (run-pln-inference)
+    PLN -> AS: Execute inference cycle
+    AS -> Scheme: Return inference results
+end
+
+Scheme -> User: Display results
+
+== Persistence ==
+User -> Storage: Save system state
+Storage -> AS: Serialize AtomSpace to JSON
+Storage -> RR: Serialize RR hypergraph to JSON
+Storage -> Storage: Consolidate memory (remove low-confidence atoms)
+Storage -> User: Confirm persistence complete
+
+@enduml
+```
+
+## RR Trialectic Dynamics Process
+
+```plantuml
+@startuml RR-Trialectic-Process
+!theme plain
+title RR Trialectic Co-Constitution Process
+
+participant "Agent Membrane" as Agent
+participant "Arena Membrane" as Arena
+participant "Relation Component" as Relation
+participant "Trialectic Engine" as Engine
+
+== Initial State ==
+Agent -> Engine: Initial salience, affordance potential
+Arena -> Engine: Initial salience, affordance potential  
+Relation -> Engine: Initial coupling strength
+
+== Trialectic Update Cycle ==
+loop Continuous Evolution
+    Engine -> Engine: Compute trialectic state vector
+    note right: [x, y, z] representing agent-arena-relation
+    
+    Engine -> Agent: Update based on arena + relation influence
+    note right: new_state[i] += coupling * (state[next] - state[prev]) / 2
+    
+    Engine -> Arena: Update based on agent + relation influence
+    Engine -> Relation: Update based on agent + arena influence
+    
+    Agent -> Engine: Updated salience
+    Arena -> Engine: Updated affordance realization
+    Relation -> Engine: Updated coupling strength
+    
+    Engine -> Engine: Apply tanh normalization
+    note right: Keep states bounded in [-1, 1]
+    
+    Engine -> Engine: Compute trialectic coherence
+    note right: coherence = Σ(state[i] * state[next]) / n
+    
+    alt High Coherence (> 0.6)
+        Engine -> Engine: Amplify co-constitution effects
+        note right: Positive feedback loop
+    else Low Coherence (< 0.3)
+        Engine -> Engine: Dampen interactions
+        note right: Prevent instability
+    end
+    
+    Engine -> Engine: Update relevance gradient
+    note right: ∇ℜ = log(affordance_realization / affordance_potential)
+end
+
+@enduml
+```
+
+## PLN Inference Process Flow
+
+```plantuml
+@startuml PLN-Inference-Process
+!theme plain
+title PLN Inference Engine Process Flow
+
+participant "RR Hypergraph" as RR
+participant "PLN Engine" as PLN
+participant "AtomSpace" as AS
+participant "Implication Generator" as ImpGen
+participant "Deduction Engine" as Ded
+participant "Abduction Engine" as Abd
+
+== Implication Generation ==
+RR -> PLN: High-coupling agent-arena pairs
+PLN -> ImpGen: Agent-arena relationship data
+ImpGen -> AS: Find corresponding atoms
+AS -> ImpGen: Agent and arena atom IDs
+
+ImpGen -> ImpGen: Calculate implication strength
+note right: strength = coupling_strength
+ImpGen -> ImpGen: Calculate implication confidence  
+note right: confidence = min(agent_salience, arena_salience)
+
+ImpGen -> AS: Create implication link
+note right: Agent → Arena with (strength, confidence)
+
+== Deduction Cycle ==
+PLN -> AS: Find all implication links
+AS -> PLN: Implication atoms
+
+loop For each implication A→B
+    PLN -> AS: Find atoms matching antecedent A
+    AS -> PLN: Antecedent instances with truth values
+    
+    alt Antecedent strength > 0.7
+        PLN -> Ded: Apply deduction rule
+        Ded -> Ded: Calculate consequent truth value
+        note right: TV(B) = TV(A→B) ⋅ TV(A)\nstrength = impl_strength ⋅ ant_strength\nconfidence = min(impl_conf, ant_conf)
+        
+        Ded -> AS: Update consequent truth value
+        AS -> PLN: Confirm update
+        PLN -> PLN: Record new conclusion
+    end
+end
+
+== Abduction Cycle ==
+loop For each implication A→B
+    PLN -> AS: Find atoms matching consequent B
+    AS -> PLN: Consequent instances with truth values
+    
+    alt Consequent strength > 0.7
+        PLN -> Abd: Apply abduction rule
+        Abd -> Abd: Calculate antecedent hypothesis
+        note right: TV(A) = TV(B) ⋅ TV(A→B) ⋅ 0.8\nReduced confidence: 0.6 factor
+        
+        Abd -> AS: Update antecedent as hypothesis
+        AS -> PLN: Confirm hypothesis
+        PLN -> PLN: Record new hypothesis
+    end
+end
+
+== Results Integration ==
+PLN -> RR: Return inference results summary
+RR -> RR: Integrate PLN feedback into RR dynamics
+
+@enduml
+```
+
+## Scheme Interface Command Processing
+
+```plantuml
+@startuml Scheme-Command-Process
+!theme plain
+title Scheme Interface Command Processing
+
+actor User
+participant "Scheme REPL" as REPL
+participant "Expression Parser" as Parser
+participant "Command Router" as Router
+participant "RR Interface" as RRInt
+participant "AtomSpace Interface" as ASInt
+participant "PLN Interface" as PLNInt
+
+== Command Input ==
+User -> REPL: Enter Scheme expression
+REPL -> Parser: Parse expression string
+Parser -> Parser: Tokenize and validate syntax
+
+alt Valid Expression
+    Parser -> Router: Parsed command structure
+else Invalid Expression
+    Parser -> REPL: Syntax error message
+    REPL -> User: Display error
+end
+
+== Command Routing ==
+Router -> Router: Identify command type
+
+alt RR Query Commands
+    Router -> RRInt: (list-rr-nodes)
+    RRInt -> RRInt: Collect all RR nodes
+    RRInt -> Router: Formatted node list
+    
+    Router -> RRInt: (get-salience node-ID)
+    RRInt -> RRInt: Look up specific node
+    RRInt -> Router: Node salience value
+    
+    Router -> RRInt: (get-system-relevance)
+    RRInt -> RRInt: Compute average relevance gradient
+    RRInt -> Router: System-wide relevance
+
+else AtomSpace Query Commands
+    Router -> ASInt: (list-atoms)
+    ASInt -> ASInt: Iterate through atom registry
+    ASInt -> Router: Formatted atom list
+    
+    Router -> ASInt: (find-atom "name")
+    ASInt -> ASInt: Search atoms by name pattern
+    ASInt -> Router: Matching atoms
+
+else Update Commands
+    Router -> RRInt: (update-salience node-ID value)
+    RRInt -> RRInt: Validate node ID and value
+    RRInt -> RRInt: Update node salience
+    RRInt -> Router: Update confirmation
+
+else Inference Commands
+    Router -> PLNInt: (run-pln-inference)
+    PLNInt -> PLNInt: Execute full inference cycle
+    PLNInt -> Router: Inference results summary
+    
+    Router -> RRInt: (find-patterns)
+    RRInt -> RRInt: Analyze RR emergence patterns
+    RRInt -> Router: Detected patterns
+
+else Unknown Command
+    Router -> REPL: Unknown command error
+end
+
+== Response Formatting ==
+Router -> REPL: Command result
+REPL -> REPL: Format as Scheme-style output
+REPL -> User: Display formatted result
+
+@enduml
+```
+
+## Persistent Storage Process Flow
+
+```plantuml
+@startuml Persistent-Storage-Process
+!theme plain
+title Persistent Storage and Memory Consolidation
+
+participant "User Request" as User
+participant "Storage Manager" as Storage
+participant "AtomSpace Serializer" as ASSerial
+participant "RR Serializer" as RRSerial  
+participant "JSON Writer" as JSON
+participant "Memory Consolidator" as Consolidator
+participant "File System" as FS
+
+== Save Operation ==
+User -> Storage: Request save to file
+Storage -> ASSerial: Serialize AtomSpace
+Storage -> RRSerial: Serialize RR hypergraph
+
+== AtomSpace Serialization ==
+ASSerial -> ASSerial: Iterate through atoms
+loop For each atom
+    ASSerial -> JSON: Write atom metadata
+    note right: {"id": N, "type": T, "name": "X"}
+    ASSerial -> JSON: Write truth values  
+    note right: "strength": S, "confidence": C
+    ASSerial -> JSON: Write outgoing links
+    note right: "outgoing": [id1, id2, ...]
+end
+ASSerial -> JSON: Write next_atom_id
+ASSerial -> Storage: AtomSpace JSON ready
+
+== RR Hypergraph Serialization ==
+RRSerial -> RRSerial: Iterate through RR nodes
+loop For each RR node
+    RRSerial -> JSON: Write node properties
+    note right: id, type, aar_type, label
+    RRSerial -> JSON: Write RR dynamics
+    note right: salience, affordance_potential, affordance_realization
+    RRSerial -> JSON: Write trialectic state
+    note right: [x, y, z] vector
+end
+
+RRSerial -> RRSerial: Iterate through RR edges
+loop For each RR edge  
+    RRSerial -> JSON: Write edge properties
+    note right: id, type, from_node, to_node, strength
+end
+RRSerial -> Storage: RR JSON ready
+
+== Memory Consolidation ==
+Storage -> Consolidator: Request memory optimization
+Consolidator -> Consolidator: Analyze atom confidence levels
+
+loop For each atom
+    alt Confidence < threshold (0.3)
+        Consolidator -> Consolidator: Mark for removal
+        note right: Low-confidence atoms are pruned
+    else Confidence >= threshold
+        Consolidator -> Consolidator: Keep in active memory
+    end
+end
+
+Consolidator -> Consolidator: Remove marked atoms
+Consolidator -> Storage: Report consolidation results
+
+== File Writing ==
+Storage -> FS: Write AtomSpace JSON file
+Storage -> FS: Write RR hypergraph JSON file
+FS -> Storage: Confirm file creation
+Storage -> User: Save operation complete
+
+== Load Operation ==
+User -> Storage: Request load from file
+Storage -> FS: Read AtomSpace JSON file
+Storage -> FS: Read RR hypergraph JSON file
+FS -> Storage: Return file contents
+
+Storage -> ASSerial: Deserialize AtomSpace
+Storage -> RRSerial: Deserialize RR hypergraph
+
+ASSerial -> ASSerial: Parse JSON and recreate atoms
+RRSerial -> RRSerial: Parse JSON and recreate RR structures
+
+Storage -> User: Load operation complete
+
+@enduml
+```
+
+## Multi-Level Emergence Detection
+
+```plantuml
+@startuml Multi-Level-Emergence
+!theme plain
+title Multi-Level Emergence Detection Process
+
+participant "Emergence Monitor" as Monitor
+participant "Agent Tracker" as AgentTrack
+participant "Arena Tracker" as ArenaTrack
+participant "Coupling Analyzer" as Coupling
+participant "Coherence Calculator" as Coherence
+participant "Pattern Recognizer" as Pattern
+participant "Emergent Relation Creator" as Creator
+
+== Continuous Monitoring ==
+loop System Evolution
+    Monitor -> AgentTrack: Check all agent nodes
+    
+    AgentTrack -> AgentTrack: Scan agent salience levels
+    loop For each agent
+        alt Salience > 0.8
+            AgentTrack -> Monitor: High-salience agent detected
+            Monitor -> ArenaTrack: Find coupled arenas for agent
+            
+            ArenaTrack -> Coupling: Analyze agent-arena pairs
+            loop For each arena
+                Coupling -> Coupling: Compute coupling strength
+                note right: strength = Σ(edge_weights) / edge_count
+                
+                alt Coupling > 0.8
+                    Coupling -> Monitor: Strong coupling detected
+                    Monitor -> Coherence: Calculate trialectic coherence
+                    
+                    Coherence -> Coherence: Measure state correlations
+                    note right: coherence = Σ(state[i] * state[next]) / n
+                    
+                    alt Coherence > 0.6
+                        Coherence -> Pattern: Emergent pattern candidate
+                        Pattern -> Pattern: Validate emergence criteria
+                        
+                        Pattern -> Pattern: Check temporal consistency
+                        Pattern -> Pattern: Verify cross-level interactions
+                        
+                        alt All criteria met
+                            Pattern -> Creator: Create emergent relation
+                            Creator -> Creator: Generate new relation node
+                            note right: Type = EMERGENT, connects agent-arena
+                            Creator -> Creator: Set emergent properties
+                            note right: salience = (agent + arena) * 0.5\naffordance_realization = 1.0
+                            Creator -> Monitor: Emergence event recorded
+                        end
+                    end
+                end
+            end
+        end
+    end
+    
+    Monitor -> Monitor: Update emergence statistics
+    Monitor -> Monitor: Log system evolution metrics
+end
+
+@enduml
+```
+
+## Integration Test Flow
+
+```plantuml
+@startuml Integration-Test-Flow
+!theme plain
+title RR-RNN Integration Test Process
+
+participant "Test Runner" as Test
+participant "RR Enhanced Test" as RRTest
+participant "Next Directions Test" as NDTest
+participant "Demo REPL Test" as REPLTest
+participant "Validation Engine" as Validator
+
+== Test Initialization ==
+Test -> Test: Setup test environment
+Test -> RRTest: Initialize basic RR test
+Test -> NDTest: Initialize comprehensive test
+Test -> REPLTest: Initialize REPL demo test
+
+== Basic RR Enhanced Test ==
+Test -> RRTest: Run test_rr_enhanced
+RRTest -> RRTest: Create RR hypergraph
+RRTest -> RRTest: Add test membranes (agent, arena, environment)
+RRTest -> RRTest: Create AtomSpace integration
+RRTest -> RRTest: Run 50 simulation steps
+
+loop 10-step intervals
+    RRTest -> RRTest: Update RR dynamics
+    RRTest -> RRTest: Sync with AtomSpace
+    RRTest -> RRTest: Check for emergent patterns
+    RRTest -> Validator: Validate state consistency
+end
+
+RRTest -> RRTest: Compute final system relevance
+RRTest -> Test: Basic test results
+
+== Comprehensive Next Directions Test ==
+Test -> NDTest: Run test_next_directions
+NDTest -> NDTest: Setup comprehensive environment
+
+NDTest -> NDTest: Test PLN Integration
+note right: Generate implications, run inference cycles
+NDTest -> NDTest: Test Scheme Interface  
+note right: Execute 8+ command types
+NDTest -> NDTest: Test Persistent Storage
+note right: Save/load, memory consolidation
+NDTest -> NDTest: Test Multi-Level Integration
+note right: Hierarchical structures, emergence detection
+
+NDTest -> Validator: Validate all subsystem interactions
+NDTest -> Test: Comprehensive test results
+
+== REPL Demo Test ==
+Test -> REPLTest: Run demo_repl
+REPLTest -> REPLTest: Create test RR environment
+REPLTest -> REPLTest: Start Scheme evaluator
+REPLTest -> REPLTest: Execute demo command sequence
+
+loop Demo commands
+    REPLTest -> REPLTest: (list-rr-nodes)
+    REPLTest -> REPLTest: (get-system-relevance)  
+    REPLTest -> REPLTest: (find-patterns)
+    REPLTest -> REPLTest: (get-salience node-1)
+    REPLTest -> Validator: Validate command responses
+end
+
+REPLTest -> Test: REPL test results
+
+== Final Validation ==
+Test -> Validator: Aggregate all test results
+Validator -> Validator: Check implementation completeness
+note right: ✓ PLN Integration\n✓ Scheme Interface\n✓ Persistent Storage\n✓ Multi-Level Integration
+
+Validator -> Validator: Verify system stability
+Validator -> Validator: Confirm feature integration
+Validator -> Test: Final validation report
+
+Test -> Test: Generate test summary
+note right: All Next Development Directions\nsuccessfully implemented and tested
+
+@enduml
+```
+
+These PlantUML diagrams provide detailed process flows for all major components of the RR-RNN system, showing the intricate interactions between relevance realization dynamics, symbolic reasoning, and cognitive architecture integration.
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