Unified framework for P-systems, M-systems (Morphogenetic Systems), Relevance Realization, and OpenCog AGI — all expressed as membrane computing models.

Consolidates code and best features from:

• ReZorg/plingua — Core P-Lingua compiler/simulator
• ReZorg/Cytos — C# M-systems simulator (reference XML examples)
• ReZorg/RRR-P-Sys-Cog — RR + OpenCog AGI extensions
• cogpy/rrpling — RR-RNN enhanced P-Lingua

• Linux OS (tested on Ubuntu 16.04+)
• GCC 4.9.0 or higher (with support for regex)
• Flex, Bison
• libboost-filesystem-dev, libboost-program-options-dev

sudo apt-get install build-essential flex bison libboost-filesystem-dev libboost-program-options-dev

make grammar      # Generate parser from Flex/Bison
make compiler     # Build bin/plingua (P-Lingua compiler)
make simulator    # Build bin/psim (P-system simulator)
make mcompiler    # Build bin/mlingua (M-Lingua compiler)
make msimulator   # Build bin/msim (M-system simulator)
make extensions   # Build RR/OpenCog demos and tests
make all          # Build everything
sudo make install

┌─────────────────────────────────────────────────────────┐
│                 Consolidated P-Lingua                    │
├──────────┬──────────┬──────────────┬────────────────────┤
│ P-Lingua │ M-Lingua │  Relevance   │   OpenCog AGI      │
│  (.pli)  │  (.mli)  │ Realization  │ (AtomSpace, PLN,   │
│          │          │ (RR-RNN)     │  ECAN, MOSES,      │
│ Parser   │ Parser   │              │  OpenPsi, Scheme)  │
│ Compiler │ Compiler │ Hypergraph   │                    │
│ Simulator│ Simulator│ Dynamics     │ Cognitive Cycles   │
├──────────┴──────────┴──────────────┴────────────────────┤
│        Cereal Serialization / Cytos XML Export           │
└─────────────────────────────────────────────────────────┘

Standard membrane computing models: transition, active membranes, tissue, SAT, PDP, SNP.

• Existing runnable models: examples/
• TODO backlog catalog (by P-system type, application category, complexity): examples/TODO_EXAMPLES_CATALOG.md

M-Lingua (.mli) extends P-Lingua with support for Morphogenetic Systems — computational models combining membrane computing with spatial geometry and polytopic tile self-assembly (based on Sosík et al. and the Cytos simulator).

• @msystem<morphogenetic> — Model declaration for M systems
• @tiling block — Tile definitions with connectors, glues, and spatial properties
• @floating — Floating object definitions with mobility and concentration
• @protion — Protein-like markers on tiles
• Rule types: @create, @destroy, @divide, metabolic rules
• Cytos-compatible XML output for Unity visualization

Original Cytos simulator XML examples in examples/cytos_xml/ for cross-validation.

See docs/MLINGUA_SPEC.md for the full M-Lingua language specification.

R-Lingua is the Relevance Realization DSL — a language extension focused on Vervaeke's Relevance Realization theory with the trielectic ennead architecture. It sits alongside P-Lingua (.pli) and M-Lingua (.mli) without changing either existing pipeline.

# Compiler binary
make rcompiler           # produces bin/rlingua

# Run unit + integration tests
make bin/test_rlingua
./bin/test_rlingua       # 73 tests

# Compile and run 50 RR dynamics steps on a .rli model
bin/rlingua examples/rr/minimal_ennead.rli -s 50 -v -o report.json

# Options:
#   -s <steps>   Run N dynamics steps (default: 0)
#   -o <file>    Output JSON grip report (default: stdout)
#   -v           Verbose per-step output
#   -h           Help

@rmodel<relevance_realization>

@ennead {
    @triad_a { identity_continuity=0.7; skill_readiness=0.6; motivational_valence=0.8; }
    @triad_b { constraint_clarity=0.5; affordance_density=0.9; feedback_latency=0.3; }
    @triad_c { coupling_strength=0.7; reciprocal_shaping=0.6; adaptive_fit=0.5; }
}

@constraints { grip_threshold=0.3; emergence_sensitivity=0.75; convergence_window=50; }

def main() {
    @agent id=a1 label="agent" salience=0.8 affordance=1.0;
    @arena id=e1 label="arena" salience=0.6 affordance=1.2;
    @coupling { a1 <-> e1 :: co_constitution strength=0.8; }
}

@observe { sample_period=10; report_fields=grip_index, ennead_balance; }

See docs/RLINGUA_SPEC.md for the full R-Lingua language specification.

Implements the Agent-Arena-Relation (AAR) trialectic framework from Vervaeke's Relevance Realization theory as membrane computing dynamics.

• RR Hypergraph — Nodes (MEMBRANE, RULE, OBJECT, ENVIRONMENT) with salience, affordance, trialectic state
• AAR Dynamics — Agent-Arena-Relation co-constitution with bidirectional coupling
• Relevance Gradient — ∇ℜ = log(affordance_realization / affordance_potential)
• Emergent Pattern Detection — High-salience cluster identification
• AtomSpace Integration — Bidirectional bridge between RR hypergraph and OpenCog AtomSpace

bin/rr_simple_demo          # Basic RR dynamics
bin/rr_demo                 # Full AAR demo
bin/demo_repl               # Interactive Scheme REPL for RR/AtomSpace
bin/test_rr_enhanced        # RR test suite
bin/test_next_directions    # Extended RR tests

Complete OpenCog cognitive architecture expressed as pure P-Lingua membrane computing models with C++ simulation bridges.

• Perception → Cognition → Action cognitive cycle
• PLN Inference — Deduction, abduction, conjunction, disjunction, implication
• ECAN Attention — STI/LTI spreading activation, rent/wage economics, attentional focus
• MOSES Evolution — Combo program trees, deme-based evolutionary search, RR-guided feature selection
• OpenPsi Drives — Competence, integrity, exploration motivational drives
• Scheme REPL — Interactive exploration of RR hypergraph and AtomSpace
• Persistence — JSON serialization for AtomSpace and RR hypergraph state

bin/test_opencog_integration   # 88 tests covering all subsystems

The platform supports the Cognitive Cities triad architecture:

include/
├── msystem/          # M-Lingua headers (parser, simulator, Cytos XML)
├── rlingua/          # R-Lingua headers (rli_parser.hpp)
├── parser/           # P-Lingua parser headers
├── simulator/        # P-system simulator headers
├── cereal/           # Serialization library
├── relevance_realization.hpp  # RR hypergraph, ennead state, grip metrics
├── rr_simulator.hpp           # RR-enhanced simulator
├── atomspace_integration.hpp  # OpenCog AtomSpace bridge + ennead projection
├── pln_integration.hpp        # Probabilistic Logic Networks
├── ecan_integration.hpp       # Economic Attention Networks
├── moses_integration.hpp      # MOSES evolutionary search
├── opencog_agi.hpp            # Unified AGI cognitive engine
├── scheme_interface.hpp       # Scheme REPL interface + ennead/grip commands
└── persistent_atomspace.hpp   # JSON persistence + ennead state

src/
├── parser/           # P-Lingua Flex/Bison parser
├── simulator/        # P-system simulator
├── msystem/          # M-Lingua parser, compiler, simulator
├── rlingua/          # R-Lingua parser (rli_parser.cpp, rlingua_main.cpp)
├── rr/               # RR/OpenCog test/demo sources
└── generators/       # Code generators

examples/
├── *.pli             # P-Lingua models (34+ examples)
├── msystem/          # M-Lingua models (6 examples)
├── rr/               # RR demos and models
├── opencog/          # OpenCog P-Lingua models (6 subsystems)
└── cytos_xml/        # Cytos reference XML (8 examples + schema)