{
  "version": "1.0.0",
  "created_at": "2026-02-17T16:48:07",
  "saved_at": "2026-02-17T16:48:07",
  "source": "standalone_package",
  "files_indexed": 106,
  "basins_populated": 72,
  "tokens": {
    "86D14520": {
      "file_path": "cubesquare\\__main__.py",
      "content_hash": 10427720240302923012,
      "topics": [
        "cubesquare",
        "main",
        "entry",
        "point",
        "python"
      ],
      "basin": 109,
      "layer": 1,
      "summaries": {
        "k0": "from .cli import main  if __name__ == \"__main__\":     main()",
        "k4": "from .cli import main  if __name__ == \"__main__\":     main()",
        "k8": "from .cli import main  if __name__ == \"__main__\":     main()"
      },
      "api_refs": []
    },
    "E5438FBE": {
      "file_path": "cubesquare\\ui.py",
      "content_hash": 7197840621579191390,
      "topics": [
        "cubesquare",
        "launch"
      ],
      "basin": 84,
      "layer": 6,
      "summaries": {
        "k0": "Cubesquare UI Launcher  Launches the internal visualizer in the default web browser.",
        "k4": "Cubesquare UI Launcher  Launches the internal visualizer in the default web browser.",
        "k8": "Cubesquare UI Launcher  Launches the internal visualizer in the default web brow"
      },
      "api_refs": []
    },
    "A1138F7F": {
      "file_path": "cubesquare\\session.py",
      "content_hash": 5600235412587150569,
      "topics": [
        "cubesquare",
        "session",
        "sessionhelper",
        "save",
        "load",
        "clear"
      ],
      "basin": 17,
      "layer": 2,
      "summaries": {
        "k0": "Cubesquare Session Helper  Simplifies agent state persistence in the agent_sandbox.",
        "k4": "Cubesquare Session Helper  Simplifies agent state persistence in the agent_sandbox.",
        "k8": "Cubesquare Session Helper  Simplifies agent state persistence in the agent_sandb"
      },
      "api_refs": []
    },
    "06F187FF": {
      "file_path": "cubesquare\\explain.py",
      "content_hash": 3723918317638286098,
      "topics": [
        "cubesquare",
        "explain",
        "tokenphysicsprofile",
        "deepexplainer",
        "analyze_token"
      ],
      "basin": 111,
      "layer": 1,
      "summaries": {
        "k0": "Cubesquare Deep Diagnostic Tool  Orchestrates multiple shells to provide a semantic physics report for a token.",
        "k4": "Cubesquare Deep Diagnostic Tool  Orchestrates multiple shells to provide a semantic physics report for a token.",
        "k8": "Cubesquare Deep Diagnostic Tool  Orchestrates multiple shells to provide a seman"
      },
      "api_refs": []
    },
    "07323759": {
      "file_path": "cubesquare\\population.py",
      "content_hash": 11354636406280097582,
      "topics": [
        "cubesquare",
        "population",
        "basin",
        "strategy",
        "semantic",
        "layer",
        "deterministic",
        "coordinates",
        "basinsemantic",
        "populationsummary",
        "basinpopulator"
      ],
      "basin": 115,
      "layer": 1,
      "summaries": {
        "k0": "Basin Population Strategy -- Semantic Layer on Deterministic Coordinates  Populates the 131 Fernandez basins with semantic meaning. Each basin gets a domain, representative terms, and I-Logic state derived from its layer position.  ARCHITECTURE:     Content -> Morton coords -> basin (mod 131) -> layer (basin * 9 // 131 + 1)          This module adds MEANING on top:     - Layer-derived semantic domains (Structure, Meaning, Location, ...)     - Term collection per basin (discovers what content clu",
        "k4": "Basin Population Strategy -- Semantic Layer on Deterministic Coordinates  Populates the 131 Fernandez basins with semantic meaning. Each basin gets a domain, representative terms, and I-Logic state de",
        "k8": "Basin Population Strategy -- Semantic Layer on Deterministic Coordinates  Popula"
      },
      "api_refs": []
    },
    "215280CD": {
      "file_path": "cubesquare\\swarm.py",
      "content_hash": 3835100813360132382,
      "topics": [
        "cubesquare",
        "swarm",
        "agent",
        "agents",
        "with",
        "logic",
        "routing",
        "agentrole",
        "dispatchresult",
        "workflowresult",
        "to_dict"
      ],
      "basin": 21,
      "layer": 2,
      "summaries": {
        "k0": "Agent Swarm -- 19 Agents with I-Logic Routing  Each agent occupies a position in Morton space. Its behavior is determined by its I-Logic state. Tasks are routed via algebraic composition -- multiply(task_state, agent_state) predicts the outcome BEFORE execution.  The 19 agents map to the 12-layer architecture:     L1-L9: 2 agents per internal layer (sensor + actor)     L10:   1 agent (Identifier -- self-awareness)     = 19 total  ROUTING PRINCIPLE:     Task arrives with an I-Logic state (conditi",
        "k4": "Agent Swarm -- 19 Agents with I-Logic Routing  Each agent occupies a position in Morton space. Its behavior is determined by its I-Logic state. Tasks are routed via algebraic composition -- multiply(t",
        "k8": "Agent Swarm -- 19 Agents with I-Logic Routing  Each agent occupies a position in"
      },
      "api_refs": []
    },
    "9032A779": {
      "file_path": "cubesquare\\training.py",
      "content_hash": 3670618271522135410,
      "topics": [
        "cubesquare",
        "training",
        "learning",
        "loop",
        "reinforcement",
        "with",
        "logic",
        "state",
        "transitions",
        "transition",
        "episode",
        "routingentry",
        "trainingloop",
        "to_dict",
        "success_rate",
        "compute_reward"
      ],
      "basin": 3,
      "layer": 1,
      "summaries": {
        "k0": "Learning Loop -- Reinforcement Learning with I-Logic State Transitions  The state space is deterministic (basin, layer, I-Logic state). The action space is I-Logic multiplication (5 possible transitions). The reward is algebraic: DIRECT = +1 (resolution), ABSORBED = -1 (dead end).  This is NOT neural RL. The I-Logic multiplication table IS the policy. What the learning loop discovers is:     1. Which agents handle which basins best (specialization)     2. Which agent sequences resolve problems (",
        "k4": "Learning Loop -- Reinforcement Learning with I-Logic State Transitions  The state space is deterministic (basin, layer, I-Logic state). The action space is I-Logic multiplication (5 possible transitio",
        "k8": "Learning Loop -- Reinforcement Learning with I-Logic State Transitions  The stat"
      },
      "api_refs": []
    },
    "17B383B7": {
      "file_path": "cubesquare\\memory.py",
      "content_hash": 8051981418144428018,
      "topics": [
        "cubesquare",
        "memory",
        "cstmemory",
        "high",
        "level",
        "write"
      ],
      "basin": 123,
      "layer": 1,
      "summaries": {
        "k0": "Cubesquare CSTMemory - High-Level API  The main interface for semantic memory operations.",
        "k4": "Cubesquare CSTMemory - High-Level API  The main interface for semantic memory operations.",
        "k8": "Cubesquare CSTMemory - High-Level API  The main interface for semantic memory op"
      },
      "api_refs": []
    },
    "43638FFF": {
      "file_path": "cubesquare\\__init__.py",
      "content_hash": 921262161705727824,
      "topics": [
        "cubesquare",
        "instant",
        "semantic",
        "memory",
        "status"
      ],
      "basin": 54,
      "layer": 4,
      "summaries": {
        "k0": "Cubesquare - Instant Semantic Memory  The semantic memory system built for production AI. 83M ops/sec. 0.04ms queries. 100% deterministic.  Quick Start:     from cubesquare import CSTMemory      memory = CSTMemory()     memory.write(\"/src/auth.py\")              # 5.97 nanoseconds     results = memory.query(\"authentication\")  # 0.04ms     print(results[0].basin)                   # 42 - semantic cluster  Layers:     memory.L1  # Geometric - file/folder hierarchy     memory.L2  # Semantic - meanin",
        "k4": "Cubesquare - Instant Semantic Memory  The semantic memory system built for production AI. 83M ops/sec. 0.04ms queries. 100% deterministic.  Quick Start:     from cubesquare import CSTMemory      memor",
        "k8": "Cubesquare - Instant Semantic Memory  The semantic memory system built for produ"
      },
      "api_refs": []
    },
    "9082AB6F": {
      "file_path": "cubesquare\\cli.py",
      "content_hash": 11631728128742297876,
      "topics": [
        "cubesquare",
        "cli",
        "cmd_ui",
        "cmd_explain",
        "cmd_mcp"
      ],
      "basin": 8,
      "layer": 1,
      "summaries": {
        "k0": "Cubesquare CLI  Command-line interface for cubesquare standalone package. Routes to 7 core shells: cst, i_logic, circular, primitives, predict, beehive, performance Includes MCP server for Claude Desktop, Cursor, and other MCP clients.",
        "k4": "Cubesquare CLI  Command-line interface for cubesquare standalone package. Routes to 7 core shells: cst, i_logic, circular, primitives, predict, beehive, performance Includes MCP server for Claude Desk",
        "k8": "Cubesquare CLI  Command-line interface for cubesquare standalone package. Routes"
      },
      "api_refs": []
    },
    "65331FF7": {
      "file_path": "cubesquare\\rebuild_index.py",
      "content_hash": 8015577743951578073,
      "topics": [
        "cubesquare",
        "rebuild",
        "index",
        "compute_file_hash",
        "extract_topics",
        "generate_summary",
        "path_to_hex_id",
        "rebuild_index"
      ],
      "basin": 83,
      "layer": 6,
      "summaries": {
        "k0": "Rebuild Beehive Index from Standalone Package Files  Creates a fresh beehive_index.json from: - cubesquare/*.py - Package source code - examples/*.py - Example scripts - docs/*.md - Documentation  NO PYTHON FOR-LOOPS in hot path. Index building is setup (bounded), not hot path.",
        "k4": "Rebuild Beehive Index from Standalone Package Files  Creates a fresh beehive_index.json from: - cubesquare/*.py - Package source code - examples/*.py - Example scripts - docs/*.md - Documentation  NO ",
        "k8": "Rebuild Beehive Index from Standalone Package Files  Creates a fresh beehive_ind"
      },
      "api_refs": []
    },
    "F5903CBA": {
      "file_path": "cubesquare\\circular\\loop_detector.py",
      "content_hash": 879289540204479195,
      "topics": [
        "cubesquare",
        "circular",
        "loop",
        "detector",
        "loopstability",
        "circularrefresult",
        "circularloopdetector",
        "to_dict",
        "load_graph",
        "detect_loop"
      ],
      "basin": 89,
      "layer": 7,
      "summaries": {
        "k0": "Circular Loop Detector - Pure Python Implementation Standalone version for cubesquare package.  Detects circular relationships via BFS traversal.",
        "k4": "Circular Loop Detector - Pure Python Implementation Standalone version for cubesquare package.  Detects circular relationships via BFS traversal.",
        "k8": "Circular Loop Detector - Pure Python Implementation Standalone version for cubes"
      },
      "api_refs": []
    },
    "E4E20F2D": {
      "file_path": "cubesquare\\circular\\srl_integration.py",
      "content_hash": 5129491443244669643,
      "topics": [
        "cubesquare",
        "circular",
        "srl",
        "integration",
        "srl_distance",
        "bounded_sqrt",
        "srl_pathfind",
        "srl_div_zero_path",
        "srl_phi_depth",
        "srl_k5_boundary",
        "srl_morton_encode",
        "part_by_3"
      ],
      "basin": 78,
      "layer": 6,
      "summaries": {
        "k0": "SRL Integration - Self-Referential Loop Pathfinding Standalone version for cubesquare package.  SRL Formula: t = d/t -> t^2 = d -> t = sqrt(d) O(1) computation via Python math.isqrt.",
        "k4": "SRL Integration - Self-Referential Loop Pathfinding Standalone version for cubesquare package.  SRL Formula: t = d/t -> t^2 = d -> t = sqrt(d) O(1) computation via Python math.isqrt.",
        "k8": "SRL Integration - Self-Referential Loop Pathfinding Standalone version for cubes"
      },
      "api_refs": []
    },
    "10038759": {
      "file_path": "cubesquare\\circular\\state_machine.py",
      "content_hash": 16400458214445935766,
      "topics": [
        "cubesquare",
        "circular",
        "state",
        "machine",
        "ilogicstate",
        "statetransition",
        "ilogicstatemachine",
        "to_complex",
        "magnitude",
        "is_stable",
        "get_k11_level",
        "get_intrinsic_state_from_k11",
        "get_phi_norm_distance",
        "get_sphere_coords",
        "get_wave_particle_strength",
        "hex_to_coords"
      ],
      "basin": 0,
      "layer": 1,
      "summaries": {
        "k0": "I-Logic 4-State Machine - 3D Unit Sphere Model Standalone version for cubesquare package.  Implements I-Logic 4-state system with O(1) operations.",
        "k4": "I-Logic 4-State Machine - 3D Unit Sphere Model Standalone version for cubesquare package.  Implements I-Logic 4-state system with O(1) operations.",
        "k8": "I-Logic 4-State Machine - 3D Unit Sphere Model Standalone version for cubesquare"
      },
      "api_refs": []
    },
    "7620E6BE": {
      "file_path": "cubesquare\\circular\\validation.py",
      "content_hash": 15815885400834578973,
      "topics": [
        "cubesquare",
        "circular",
        "validation",
        "validationlevel",
        "validationresult",
        "circularvalidator",
        "to_dict",
        "validate_loop",
        "validate_srl"
      ],
      "basin": 98,
      "layer": 7,
      "summaries": {
        "k0": "Circular Validation - System Integrity Checker Standalone version for cubesquare package.  Validates circular system integrity.",
        "k4": "Circular Validation - System Integrity Checker Standalone version for cubesquare package.  Validates circular system integrity.",
        "k8": "Circular Validation - System Integrity Checker Standalone version for cubesquare"
      },
      "api_refs": []
    },
    "7640E824": {
      "file_path": "cubesquare\\circular\\__init__.py",
      "content_hash": 17923060176370886076,
      "topics": [
        "cubesquare",
        "circular",
        "get_system_info"
      ],
      "basin": 100,
      "layer": 7,
      "summaries": {
        "k0": "Circular System - 3D Unit Sphere I-Logic Standalone version for cubesquare package.  Provides circular relationship detection, I-Logic 4-state stabilization, and SRL (Self-Referential Loop) pathfinding.  Core Principles: - O(1) SRL computation: t = d/t -> t = sqrt(d) - I-Logic 4-state machine: DIRECT/INVERSE/SPIRAL/ANTI_SPIRAL/ABSORBED - Morton Z-order encoding - BFS pathfinding with Python fallback",
        "k4": "Circular System - 3D Unit Sphere I-Logic Standalone version for cubesquare package.  Provides circular relationship detection, I-Logic 4-state stabilization, and SRL (Self-Referential Loop) pathfindin",
        "k8": "Circular System - 3D Unit Sphere I-Logic Standalone version for cubesquare packa"
      },
      "api_refs": []
    },
    "10A0EDE1": {
      "file_path": "cubesquare\\database\\abstraction.py",
      "content_hash": 18189946422300314611,
      "topics": [
        "cubesquare",
        "database",
        "abstraction",
        "databasebackend",
        "databaseerror",
        "connectionerror",
        "queryerror",
        "abstractdatabaseadapter",
        "databaseabstractionlayer",
        "databasetransaction",
        "connect",
        "disconnect",
        "execute",
        "execute_many",
        "fetch_one",
        "fetch_all",
        "begin_transaction",
        "commit",
        "rollback",
        "get_backend"
      ],
      "basin": 10,
      "layer": 1,
      "summaries": {
        "k0": "Database Abstraction Layer Standalone version for cubesquare package.  Provides backend-agnostic database interface.",
        "k4": "Database Abstraction Layer Standalone version for cubesquare package.  Provides backend-agnostic database interface.",
        "k8": "Database Abstraction Layer Standalone version for cubesquare package.  Provides "
      },
      "api_refs": []
    },
    "E4B282FD": {
      "file_path": "cubesquare\\database\\adapter.py",
      "content_hash": 7994215415009114249,
      "topics": [
        "cubesquare",
        "database",
        "adapter",
        "sqliteadapter",
        "is_connected",
        "connect",
        "disconnect",
        "execute",
        "execute_many",
        "fetch_one",
        "fetch_all"
      ],
      "basin": 75,
      "layer": 6,
      "summaries": {
        "k0": "SQLite Database Adapter Standalone version for cubesquare package.",
        "k4": "SQLite Database Adapter Standalone version for cubesquare package.",
        "k8": "SQLite Database Adapter Standalone version for cubesquare package."
      },
      "api_refs": []
    },
    "F580C7FF": {
      "file_path": "cubesquare\\database\\__init__.py",
      "content_hash": 8535187585649146443,
      "topics": [
        "cubesquare",
        "database"
      ],
      "basin": 88,
      "layer": 7,
      "summaries": {
        "k0": "Database Module - SQLite Adapter for Cubesquare Standalone version with pure Python implementation.",
        "k4": "Database Module - SQLite Adapter for Cubesquare Standalone version with pure Python implementation.",
        "k8": "Database Module - SQLite Adapter for Cubesquare Standalone version with pure Pyt"
      },
      "api_refs": []
    },
    "90806ADE": {
      "file_path": "cubesquare\\i_logic\\algebra.py",
      "content_hash": 13245782665291823204,
      "topics": [
        "cubesquare",
        "logic",
        "algebra",
        "multiply",
        "compose",
        "detect_cycle",
        "get_inverse",
        "verify_algebra"
      ],
      "basin": 8,
      "layer": 1,
      "summaries": {
        "k0": "I-Logic Algebra  O(1) multiplication table for state composition.  Multiplication Table:      | DIR  INV  SPI  ASP  ABS -----+--------------------------- DIR  |  DIR  INV  SPI  ASP  ABS INV  |  INV  DIR  ASP  SPI  ABS SPI  |  SPI  ASP  INV  DIR  ABS ASP  |  ASP  SPI  DIR  INV  ABS ABS  |  ABS  ABS  ABS  ABS  ABS",
        "k4": "I-Logic Algebra  O(1) multiplication table for state composition.  Multiplication Table:      | DIR  INV  SPI  ASP  ABS -----+--------------------------- DIR  |  DIR  INV  SPI  ASP  ABS INV  |  INV  D",
        "k8": "I-Logic Algebra  O(1) multiplication table for state composition.  Multiplicatio"
      },
      "api_refs": []
    },
    "6500C35B": {
      "file_path": "cubesquare\\i_logic\\predict.py",
      "content_hash": 12092798648193817957,
      "topics": [
        "cubesquare",
        "logic",
        "predict",
        "prediction",
        "predict_route",
        "find_resolver",
        "compose_path_string"
      ],
      "basin": 80,
      "layer": 6,
      "summaries": {
        "k0": "I-Logic Prediction  Predict routing outcomes without execution.",
        "k4": "I-Logic Prediction  Predict routing outcomes without execution.",
        "k8": "I-Logic Prediction  Predict routing outcomes without execution."
      },
      "api_refs": []
    },
    "E5438B6D": {
      "file_path": "cubesquare\\i_logic\\states.py",
      "content_hash": 12834867945138143902,
      "topics": [
        "cubesquare",
        "logic",
        "states",
        "ilogicstate",
        "name",
        "symbol",
        "from_name",
        "normalize"
      ],
      "basin": 84,
      "layer": 6,
      "summaries": {
        "k0": "I-Logic States  5 states implemented as complex numbers for natural multiplication.",
        "k4": "I-Logic States  5 states implemented as complex numbers for natural multiplication.",
        "k8": "I-Logic States  5 states implemented as complex numbers for natural multiplicati"
      },
      "api_refs": []
    },
    "F5A38DF7": {
      "file_path": "cubesquare\\i_logic\\__init__.py",
      "content_hash": 13298551402350251272,
      "topics": [
        "cubesquare",
        "logic",
        "module",
        "algebraic",
        "state",
        "composition"
      ],
      "basin": 90,
      "layer": 7,
      "summaries": {
        "k0": "I-Logic Module - Algebraic State Composition  5-state algebra for agent routing with O(1) multiplication.  States:     DIRECT (1)       - Pass through unchanged     INVERSE (-1)     - Reflect/negate     SPIRAL (+i)      - Rotate 90 degrees     ANTI_SPIRAL (-i) - Counter-rotate 90 degrees     ABSORBED (0)     - Terminate/consume  Algebraic Properties:     - Closure: Product of any two states is a state     - Associativity: (a * b) * c = a * (b * c)     - Identity: DIRECT (1) is the identity     -",
        "k4": "I-Logic Module - Algebraic State Composition  5-state algebra for agent routing with O(1) multiplication.  States:     DIRECT (1)       - Pass through unchanged     INVERSE (-1)     - Reflect/negate  ",
        "k8": "I-Logic Module - Algebraic State Composition  5-state algebra for agent routing "
      },
      "api_refs": []
    },
    "B2038DFE": {
      "file_path": "cubesquare\\layers\\base.py",
      "content_hash": 10208188816391286882,
      "topics": [
        "cubesquare",
        "layers",
        "base",
        "layer",
        "class",
        "layerid",
        "token",
        "from_morton",
        "from_path",
        "query",
        "filter",
        "navigate",
        "distance",
        "related",
        "cluster"
      ],
      "basin": 32,
      "layer": 3,
      "summaries": {
        "k0": "Cubesquare Layer Base Class  All layers share this contract for consistent API.",
        "k4": "Cubesquare Layer Base Class  All layers share this contract for consistent API.",
        "k8": "Cubesquare Layer Base Class  All layers share this contract for consistent API."
      },
      "api_refs": []
    },
    "8710A805": {
      "file_path": "cubesquare\\layers\\electromagnetic.py",
      "content_hash": 13649896729615580603,
      "topics": [
        "cubesquare",
        "layers",
        "electromagnetic",
        "layer",
        "l8",
        "query",
        "filter",
        "navigate",
        "distance",
        "polarity",
        "field_strength"
      ],
      "basin": 113,
      "layer": 1,
      "summaries": {
        "k0": "L8 ELECTROMAGNETIC Layer  Force dynamics and polarity.",
        "k4": "L8 ELECTROMAGNETIC Layer  Force dynamics and polarity.",
        "k8": "L8 ELECTROMAGNETIC Layer  Force dynamics and polarity."
      },
      "api_refs": []
    },
    "904286AC": {
      "file_path": "cubesquare\\layers\\emotional.py",
      "content_hash": 2051053304020860719,
      "topics": [
        "cubesquare",
        "layers",
        "emotional",
        "layer",
        "l6",
        "query",
        "filter",
        "navigate",
        "distance",
        "emotional_state",
        "coherence_score"
      ],
      "basin": 4,
      "layer": 1,
      "summaries": {
        "k0": "L6 EMOTIONAL Layer  Map by frequency and sentiment.",
        "k4": "L6 EMOTIONAL Layer  Map by frequency and sentiment.",
        "k8": "L6 EMOTIONAL Layer  Map by frequency and sentiment."
      },
      "api_refs": []
    },
    "17A15EB6": {
      "file_path": "cubesquare\\layers\\frequency.py",
      "content_hash": 5129243387461232851,
      "topics": [
        "cubesquare",
        "layers",
        "frequency",
        "layer",
        "l7",
        "query",
        "filter",
        "navigate",
        "distance",
        "wavelength"
      ],
      "basin": 122,
      "layer": 1,
      "summaries": {
        "k0": "L7 FREQUENCY Layer  Attention and energy mapping.",
        "k4": "L7 FREQUENCY Layer  Attention and energy mapping.",
        "k8": "L7 FREQUENCY Layer  Attention and energy mapping."
      },
      "api_refs": []
    },
    "D480A4F0": {
      "file_path": "cubesquare\\layers\\functional.py",
      "content_hash": 10799034972953548823,
      "topics": [
        "cubesquare",
        "layers",
        "functional",
        "layer",
        "l4",
        "query",
        "filter",
        "navigate",
        "distance",
        "abstraction_level"
      ],
      "basin": 72,
      "layer": 5,
      "summaries": {
        "k0": "L4 FUNCTIONAL Layer  Filter by abstraction level.",
        "k4": "L4 FUNCTIONAL Layer  Filter by abstraction level.",
        "k8": "L4 FUNCTIONAL Layer  Filter by abstraction level."
      },
      "api_refs": []
    },
    "86E309B7": {
      "file_path": "cubesquare\\layers\\geometric.py",
      "content_hash": 394517573817396618,
      "topics": [
        "cubesquare",
        "layers",
        "geometric",
        "layer",
        "l1",
        "query",
        "filter",
        "navigate",
        "distance",
        "parent",
        "children",
        "siblings",
        "depth"
      ],
      "basin": 110,
      "layer": 1,
      "summaries": {
        "k0": "L1 GEOMETRIC Layer  Navigate by file and folder hierarchy.",
        "k4": "L1 GEOMETRIC Layer  Navigate by file and folder hierarchy.",
        "k8": "L1 GEOMETRIC Layer  Navigate by file and folder hierarchy."
      },
      "api_refs": []
    },
    "E4D21DF7": {
      "file_path": "cubesquare\\layers\\membrane.py",
      "content_hash": 16423511205254338472,
      "topics": [
        "cubesquare",
        "layers",
        "membrane",
        "layer",
        "l9",
        "query",
        "filter",
        "navigate",
        "distance",
        "permeability",
        "transmission_cost",
        "heal",
        "reflect_basin"
      ],
      "basin": 77,
      "layer": 6,
      "summaries": {
        "k0": "L9 MEMBRANE Layer  Information flow and transmission.",
        "k4": "L9 MEMBRANE Layer  Information flow and transmission.",
        "k8": "L9 MEMBRANE Layer  Information flow and transmission."
      },
      "api_refs": []
    },
    "90406801": {
      "file_path": "cubesquare\\layers\\probabilistic.py",
      "content_hash": 817234573308593605,
      "topics": [
        "cubesquare",
        "layers",
        "probabilistic",
        "layer",
        "l5",
        "query",
        "filter",
        "navigate",
        "distance",
        "access_count",
        "last_access"
      ],
      "basin": 4,
      "layer": 1,
      "summaries": {
        "k0": "L5 PROBABILISTIC Layer  Match by usage patterns.",
        "k4": "L5 PROBABILISTIC Layer  Match by usage patterns.",
        "k8": "L5 PROBABILISTIC Layer  Match by usage patterns."
      },
      "api_refs": []
    },
    "F5C0193D": {
      "file_path": "cubesquare\\layers\\semantic.py",
      "content_hash": 17050169188557479835,
      "topics": [
        "cubesquare",
        "layers",
        "semantic",
        "layer",
        "l2",
        "query",
        "filter",
        "navigate",
        "distance",
        "cluster_id",
        "cluster_tokens",
        "basin_stats"
      ],
      "basin": 92,
      "layer": 7,
      "summaries": {
        "k0": "L2 SEMANTIC Layer  Query by meaning and concept using Fernandez basins.",
        "k4": "L2 SEMANTIC Layer  Query by meaning and concept using Fernandez basins.",
        "k8": "L2 SEMANTIC Layer  Query by meaning and concept using Fernandez basins."
      },
      "api_refs": []
    },
    "97702998": {
      "file_path": "cubesquare\\layers\\spatial.py",
      "content_hash": 16378204470129647746,
      "topics": [
        "cubesquare",
        "layers",
        "spatial",
        "layer",
        "l3",
        "query",
        "filter",
        "navigate",
        "distance",
        "nearby",
        "region",
        "coordinates"
      ],
      "basin": 119,
      "layer": 1,
      "summaries": {
        "k0": "L3 SPATIAL Layer  Find nearby and related content using Morton locality.",
        "k4": "L3 SPATIAL Layer  Find nearby and related content using Morton locality.",
        "k8": "L3 SPATIAL Layer  Find nearby and related content using Morton locality."
      },
      "api_refs": []
    },
    "D4330FF7": {
      "file_path": "cubesquare\\layers\\__init__.py",
      "content_hash": 7589277214455153003,
      "topics": [
        "cubesquare",
        "layers",
        "layer",
        "system",
        "get_layer_class",
        "get_layer_name"
      ],
      "basin": 67,
      "layer": 5,
      "summaries": {
        "k0": "Cubesquare CST Layer System  9 layers for navigating semantic memory:  L1 GEOMETRIC      - Navigate by file and folder hierarchy L2 SEMANTIC       - Query by meaning and concept L3 SPATIAL        - Find nearby and related content L4 FUNCTIONAL     - Filter by abstraction level L5 PROBABILISTIC  - Match by usage patterns L6 EMOTIONAL      - Map by frequency and sentiment L7 FREQUENCY      - Attention and energy mapping L8 ELECTROMAGNETIC - Force dynamics and polarity L9 MEMBRANE       - Informati",
        "k4": "Cubesquare CST Layer System  9 layers for navigating semantic memory:  L1 GEOMETRIC      - Navigate by file and folder hierarchy L2 SEMANTIC       - Query by meaning and concept L3 SPATIAL        - Fi",
        "k8": "Cubesquare CST Layer System  9 layers for navigating semantic memory:  L1 GEOMET"
      },
      "api_refs": []
    },
    "1042A353": {
      "file_path": "cubesquare\\primitives\\basin.py",
      "content_hash": 3242415629453018429,
      "topics": [
        "cubesquare",
        "primitives",
        "basin",
        "primitive",
        "fernandez",
        "clustering",
        "compute",
        "layer_from_basin",
        "basin_count",
        "basin_name"
      ],
      "basin": 4,
      "layer": 1,
      "summaries": {
        "k0": "Basin Primitive - O(1) Fernandez Clustering  Verified: 131 basins, 0.82 uniformity, 8 operations.",
        "k4": "Basin Primitive - O(1) Fernandez Clustering  Verified: 131 basins, 0.82 uniformity, 8 operations.",
        "k8": "Basin Primitive - O(1) Fernandez Clustering  Verified: 131 basins, 0.82 uniformi"
      },
      "api_refs": []
    },
    "E5038DFE": {
      "file_path": "cubesquare\\primitives\\i_logic.py",
      "content_hash": 6591770845773446901,
      "topics": [
        "cubesquare",
        "primitives",
        "logic",
        "primitive",
        "state",
        "multiplication",
        "multiply",
        "compose",
        "detect_cycle"
      ],
      "basin": 80,
      "layer": 6,
      "summaries": {
        "k0": "I-Logic Primitive - O(1) State Multiplication  Verified: 11/11 tests, 125 combinations.  5 states: DIRECT (1), INVERSE (-1), SPIRAL (+i), ANTI_SPIRAL (-i), ABSORBED (0)",
        "k4": "I-Logic Primitive - O(1) State Multiplication  Verified: 11/11 tests, 125 combinations.  5 states: DIRECT (1), INVERSE (-1), SPIRAL (+i), ANTI_SPIRAL (-i), ABSORBED (0)",
        "k8": "I-Logic Primitive - O(1) State Multiplication  Verified: 11/11 tests, 125 combin"
      },
      "api_refs": []
    },
    "21022D27": {
      "file_path": "cubesquare\\primitives\\morton.py",
      "content_hash": 3777160816847028367,
      "topics": [
        "cubesquare",
        "primitives",
        "morton",
        "primitive",
        "order",
        "encoding",
        "encode",
        "decode",
        "distance"
      ],
      "basin": 16,
      "layer": 2,
      "summaries": {
        "k0": "Morton Primitive - O(1) Z-order Encoding  Verified: 100M entries, 100% correct, 21 operations.",
        "k4": "Morton Primitive - O(1) Z-order Encoding  Verified: 100M entries, 100% correct, 21 operations.",
        "k8": "Morton Primitive - O(1) Z-order Encoding  Verified: 100M entries, 100% correct, "
      },
      "api_refs": []
    },
    "43315EDB": {
      "file_path": "cubesquare\\primitives\\srl.py",
      "content_hash": 8154845893118002496,
      "topics": [
        "cubesquare",
        "primitives",
        "srl",
        "primitive",
        "integer",
        "square",
        "root",
        "sqrt",
        "validate",
        "time_scale"
      ],
      "basin": 51,
      "layer": 4,
      "summaries": {
        "k0": "SRL Primitive - O(1) Integer Square Root  Verified: 0% error, distance up to 10^9, <=25 iterations.  The SRL formula: t = d/t -> t^2 = d -> t = sqrt(d) Loop is INSIDE the unit - self-reference stabilized.",
        "k4": "SRL Primitive - O(1) Integer Square Root  Verified: 0% error, distance up to 10^9, <=25 iterations.  The SRL formula: t = d/t -> t^2 = d -> t = sqrt(d) Loop is INSIDE the unit - self-reference stabili",
        "k8": "SRL Primitive - O(1) Integer Square Root  Verified: 0% error, distance up to 10^"
      },
      "api_refs": []
    },
    "75B18CBE": {
      "file_path": "cubesquare\\primitives\\__init__.py",
      "content_hash": 9363427706779882286,
      "topics": [
        "cubesquare",
        "primitives",
        "verified",
        "mathematical",
        "guarantees"
      ],
      "basin": 91,
      "layer": 7,
      "summaries": {
        "k0": "Verified Primitives - Mathematical Guarantees  Four O(1) primitives that form the foundation of the system:  | Primitive | Operation | Bound | Status | |-----------|-----------|-------|--------| | Morton    | 3D -> Z-order | O(1), 21 ops | Verified | | Basin     | Token -> cluster | O(1), 8 ops | Verified | | SRL       | Distance -> path | O(1), <=25 iter | Verified | | I-Logic   | State composition | O(1) * N | Verified |  Key distinction: Cost determined at algorithm design time, not query tim",
        "k4": "Verified Primitives - Mathematical Guarantees  Four O(1) primitives that form the foundation of the system:  | Primitive | Operation | Bound | Status | |-----------|-----------|-------|--------| | Mor",
        "k8": "Verified Primitives - Mathematical Guarantees  Four O(1) primitives that form th"
      },
      "api_refs": []
    },
    "43128DF7": {
      "file_path": "cubesquare\\shells\\agent.py",
      "content_hash": 8307312841529958576,
      "topics": [
        "cubesquare",
        "shells",
        "agent",
        "agentprofile",
        "agentshell",
        "morton_spread_bits",
        "morton_compact_bits",
        "morton_encode",
        "morton_decode",
        "hex_to_morton",
        "calculate_distance",
        "classify_layer",
        "generate_hex_id",
        "execute"
      ],
      "basin": 49,
      "layer": 4,
      "summaries": {
        "k0": "Agent Shell - Complete Agent Onboarding and Contextualization ============================================================== Agent Shell for cubesquare_standalone.  This shell provides agent registration, spatial tracking, and contextualization using the CST (Coordinate Space Tokenization) system.  Commands:     status          - Show system status (agents, tables, backends)     onboard         - Onboard a new agent (ID, name, type, specialization, hex)     context         - Generate agent conte",
        "k4": "Agent Shell - Complete Agent Onboarding and Contextualization ============================================================== Agent Shell for cubesquare_standalone.  This shell provides agent registrat",
        "k8": "Agent Shell - Complete Agent Onboarding and Contextualization =================="
      },
      "api_refs": []
    },
    "D3B38176": {
      "file_path": "cubesquare\\shells\\basin.py",
      "content_hash": 14582813111056781803,
      "topics": [
        "cubesquare",
        "shells",
        "basin",
        "basinanomaly",
        "basindata",
        "outerlayerinfo",
        "basinregistry",
        "basinbackend",
        "baseshell",
        "basinshell",
        "to_dict",
        "get_basin_layer"
      ],
      "basin": 59,
      "layer": 5,
      "summaries": {
        "k0": "Basin Shell - 131-Basin Fernandez System (Standalone) ====================================================== HEX_ID: 0BB10700  Standalone version of the 131-basin Fernandez system shell. Basin Shell for cubesquare_standalone.  The Fernandez system organizes tokens into 131 basins (a prime number) mapped across 9 internal layers plus 3 outer layers (L10-L12).  Mathematical Foundation:     Basin = token_hash % 131     Layer = floor(basin * 9 / 131) + 1  Features:     - O(1) basin computation via m",
        "k4": "Basin Shell - 131-Basin Fernandez System (Standalone) ====================================================== HEX_ID: 0BB10700  Standalone version of the 131-basin Fernandez system shell. Basin Shell f",
        "k8": "Basin Shell - 131-Basin Fernandez System (Standalone) =========================="
      },
      "api_refs": []
    },
    "F5B10CEF": {
      "file_path": "cubesquare\\shells\\basin_dict.py",
      "content_hash": 7894036258035465150,
      "topics": [
        "cubesquare",
        "shells",
        "basin",
        "dict",
        "basindictionary",
        "basindictshell",
        "extract_terms",
        "frequency_to_wavelength",
        "wavelength_to_basin",
        "get_wavelength_range_for_basin",
        "get_layer_for_basin"
      ],
      "basin": 91,
      "layer": 7,
      "summaries": {
        "k0": "Basin Dictionary Shell - FML Frequency-Based Basin Assignment Standalone version for cubesquare package.  HEX_ID: 0BF1DD03  CLI interface for building and querying the FML basin dictionary. Basin assignment uses frequency-derived wavelength mapping (NOT Fernandez iteration).  Hypothesis: Word frequency (Zipf's law) maps to wavelength:   - High frequency words (the, is, a) -> short wavelength -> violet -> low basin   - Low frequency words (fiber, healer) -> long wavelength -> red -> high basin  D",
        "k4": "Basin Dictionary Shell - FML Frequency-Based Basin Assignment Standalone version for cubesquare package.  HEX_ID: 0BF1DD03  CLI interface for building and querying the FML basin dictionary. Basin assi",
        "k8": "Basin Dictionary Shell - FML Frequency-Based Basin Assignment Standalone version"
      },
      "api_refs": []
    },
    "31F300D6": {
      "file_path": "cubesquare\\shells\\circular.py",
      "content_hash": 12660386185412272014,
      "topics": [
        "cubesquare",
        "shells",
        "circular",
        "circularshell",
        "status",
        "srl",
        "k11",
        "intrinsic",
        "validate_srl",
        "validate_all",
        "run"
      ],
      "basin": 31,
      "layer": 3,
      "summaries": {
        "k0": "Circular Shell - Circular System Operations Standalone version for cubesquare package.",
        "k4": "Circular Shell - Circular System Operations Standalone version for cubesquare package.",
        "k8": "Circular Shell - Circular System Operations Standalone version for cubesquare pa"
      },
      "api_refs": []
    },
    "A160EFCD": {
      "file_path": "cubesquare\\shells\\condition.py",
      "content_hash": 9949999987287376227,
      "topics": [
        "cubesquare",
        "shells",
        "condition",
        "ilogicstateenum",
        "encodedcondition",
        "conditionencoder",
        "name",
        "frequency_to_wavelength",
        "wavelength_to_basin",
        "basin_to_ilogic"
      ],
      "basin": 22,
      "layer": 2,
      "summaries": {
        "k0": "Condition Encoder Shell - Semantic Condition Encoding HEX_ID: 0BF1DD04  Standalone version for cubesquare.  Encodes semantic conditions into ephemeral hex IDs using FML frequency-derived wavelength mapping. I-Logic state is determined by GEOMETRY (basin position), not keywords.  INPUTS:     - Semantic primitive dict: {text, type, encoding}     - Plain text strings     - Condition type: state_condition, relationship, query, assertion, command  OUTPUTS:     - EncodedCondition: hex_id, basin, wavel",
        "k4": "Condition Encoder Shell - Semantic Condition Encoding HEX_ID: 0BF1DD04  Standalone version for cubesquare.  Encodes semantic conditions into ephemeral hex IDs using FML frequency-derived wavelength ma",
        "k8": "Condition Encoder Shell - Semantic Condition Encoding HEX_ID: 0BF1DD04  Standalo"
      },
      "api_refs": []
    },
    "D460A680": {
      "file_path": "cubesquare\\shells\\cst.py",
      "content_hash": 17917854677858205390,
      "topics": [
        "cubesquare",
        "shells",
        "cst",
        "cstshell",
        "status",
        "list_layers",
        "get_layer",
        "get_basin",
        "token_to_basin",
        "run"
      ],
      "basin": 70,
      "layer": 5,
      "summaries": {
        "k0": "CST Shell - Core CST Operations Standalone version for cubesquare package.",
        "k4": "CST Shell - Core CST Operations Standalone version for cubesquare package.",
        "k8": "CST Shell - Core CST Operations Standalone version for cubesquare package."
      },
      "api_refs": []
    },
    "F5B1C6DF": {
      "file_path": "cubesquare\\shells\\cypher.py",
      "content_hash": 907998620996175083,
      "topics": [
        "cubesquare",
        "shells",
        "cypher",
        "qphase",
        "contextcode",
        "validationlevel",
        "issueseverity",
        "phaseconfig",
        "contextconfig",
        "cyphermessage",
        "decoderesult",
        "validationissue",
        "validationreport",
        "usageentry",
        "usagesummary",
        "billingreport",
        "cyphervalidator",
        "cypherusagetracker",
        "cyphershell"
      ],
      "basin": 91,
      "layer": 7,
      "summaries": {
        "k0": "Cypher Shell - Encode/Decode/Validate Cypher Operations (Standalone) ===================================================================== HEX_ID: CY000200 AREA: Cypher System (CY) COMPONENT: Shell Interface (00) LEVEL: Secondary (02) INSTANCE: Primary shell (00)  Standalone cypher shell for the cubesquare package. Provides encode/decode/validate/usage commands for the cypher system. Fully self-contained.  CYPHER FORMAT:     [CONTEXT]PRIME_SEED: MESSAGE |CLR*PRIME_SEED|Q-PHASE[FREQUENCY_HZ]  COM",
        "k4": "Cypher Shell - Encode/Decode/Validate Cypher Operations (Standalone) ===================================================================== HEX_ID: CY000200 AREA: Cypher System (CY) COMPONENT: Shell In",
        "k8": "Cypher Shell - Encode/Decode/Validate Cypher Operations (Standalone) ==========="
      },
      "api_refs": []
    },
    "21015DFF": {
      "file_path": "cubesquare\\shells\\data_analysis.py",
      "content_hash": 3273780878928512844,
      "topics": [
        "cubesquare",
        "shells",
        "data",
        "analysis",
        "datapattern",
        "dataidea",
        "ecosystemnode",
        "datastructurediscovery",
        "ecosystemrelationshipanalyzer",
        "ideagenerator",
        "dataanalysisshell",
        "get_i_logic_for_category",
        "batch_categorize_basins",
        "batch_compute_morton_buckets",
        "discover_clusters"
      ],
      "basin": 16,
      "layer": 2,
      "summaries": {
        "k0": "Data Analysis Shell - Bidirectional Pattern Detection & Idea Generation HEX_ID: 44415441 (DATA - Tools/Shell/Analysis/Primary)  Standalone version for cubesquare.  INPUTS:     - Token dictionaries with hex_id, morton, basin, layer, topics     - Beehive index JSON data     - Token relationship data  OUTPUTS:     - DataPattern: pattern_id, pattern_type, description, tokens, confidence, basin, layer     - DataIdea: idea_id, idea_type, title, description, action, confidence, i_logic_state     - Clus",
        "k4": "Data Analysis Shell - Bidirectional Pattern Detection & Idea Generation HEX_ID: 44415441 (DATA - Tools/Shell/Analysis/Primary)  Standalone version for cubesquare.  INPUTS:     - Token dictionaries wit",
        "k8": "Data Analysis Shell - Bidirectional Pattern Detection & Idea Generation HEX_ID: "
      },
      "api_refs": []
    },
    "C322825B": {
      "file_path": "cubesquare\\shells\\distance.py",
      "content_hash": 3677936971581896454,
      "topics": [
        "cubesquare",
        "shells",
        "distance",
        "distanceshell",
        "hex_to_morton",
        "morton_decode_wrapped",
        "hex_to_coords",
        "euclidean_distance",
        "manhattan_distance",
        "chebyshev_distance",
        "morton_distance",
        "srl_hops",
        "time_from_distance",
        "distance_from_time",
        "compute_distance"
      ],
      "basin": 50,
      "layer": 4,
      "summaries": {
        "k0": "Distance Shell - Spatial O(1) Distance Computation ===================================================  HEX_ID: 43208FA1 AREA: Physical (43) COMPONENT: Distance (20) LEVEL: Shell (8F) INSTANCE: Secondary (A1)  Core Principle: d = t^2 (inverse of t = sqrt(d)) Distance is the squared time. SRL hops computed via log_phi lookup.  The manifold has 48^3 = 110,592 cells. Each cell has a unique Morton code. Distance between any two tokens is O(1) via Morton difference or coordinate Euclidean.  Commands:",
        "k4": "Distance Shell - Spatial O(1) Distance Computation ===================================================  HEX_ID: 43208FA1 AREA: Physical (43) COMPONENT: Distance (20) LEVEL: Shell (8F) INSTANCE: Second",
        "k8": "Distance Shell - Spatial O(1) Distance Computation ============================="
      },
      "api_refs": []
    },
    "545209A4": {
      "file_path": "cubesquare\\shells\\ecosystem.py",
      "content_hash": 14399881299785643124,
      "topics": [
        "cubesquare",
        "shells",
        "ecosystem",
        "validationstatus",
        "relationshiptype",
        "semanticcategory",
        "connectivityreport",
        "validationresult",
        "healthreport",
        "ecosystemshell",
        "from_basin",
        "to_dict"
      ],
      "basin": 69,
      "layer": 5,
      "summaries": {
        "k0": "Ecosystem Shell - Token Relationship and Connectivity Analysis HEX_ID: EC0NSH01  Standalone version for cubesquare.  INPUTS:     - Token hex IDs (8-char strings)     - Basin numbers (0-130)     - Category names (CORE, ACTION, DATA, RELATION, META)  OUTPUTS:     - Connectivity reports (total_tokens, relationships, avg_degree, bridges)     - Neighbor lists with relationship types     - Bridge statistics between categories     - Path finding between tokens     - Validation status (PASSED, WARNING, ",
        "k4": "Ecosystem Shell - Token Relationship and Connectivity Analysis HEX_ID: EC0NSH01  Standalone version for cubesquare.  INPUTS:     - Token hex IDs (8-char strings)     - Basin numbers (0-130)     - Cate",
        "k8": "Ecosystem Shell - Token Relationship and Connectivity Analysis HEX_ID: EC0NSH01 "
      },
      "api_refs": []
    },
    "90B21FB5": {
      "file_path": "cubesquare\\shells\\epicycle.py",
      "content_hash": 5069086970235571658,
      "topics": [
        "cubesquare",
        "shells",
        "epicycle",
        "epicyclestate",
        "trajectorypoint",
        "spheresection",
        "epicycleshell",
        "create_epicycle_states",
        "calculate_position_at_time",
        "generate_trajectory"
      ],
      "basin": 11,
      "layer": 1,
      "summaries": {
        "k0": "Epicycle Shell - Comprehensive Epicycle Operations ===================================================  HEX_ID: E7C50000 AREA: Epicycle (E7) COMPONENT: Core (C5) LEVEL: Shell (00) INSTANCE: Primary (00)  Standalone epicycle system integrating: - Core epicycle mathematics - K11 consciousness mapping - SRL Planck scaling - Orbital dynamics and resonance  NOTE: This is a simplified standalone version. Additional integrations (gene theory, MCP bridge, CST backend) are available in the full ecosystem",
        "k4": "Epicycle Shell - Comprehensive Epicycle Operations ===================================================  HEX_ID: E7C50000 AREA: Epicycle (E7) COMPONENT: Core (C5) LEVEL: Shell (00) INSTANCE: Primary (0",
        "k8": "Epicycle Shell - Comprehensive Epicycle Operations ============================="
      },
      "api_refs": []
    },
    "C36289BD": {
      "file_path": "cubesquare\\shells\\fml.py",
      "content_hash": 76920047979710959,
      "topics": [
        "cubesquare",
        "shells",
        "fml",
        "fmltoken",
        "fmlencoder"
      ],
      "basin": 54,
      "layer": 4,
      "summaries": {
        "k0": "FML Frequency Encoder Shell - Full 9-Layer Deterministic Token Generation HEX_ID: 0BF1DD10  Standalone version for cubesquare.  Converts any text input into a deterministic 9-layer CST token. Same input ALWAYS produces same token. This is the foundation of learning without training: deterministic encoding + .cst persistence = lookup.  INPUTS:     - Text string to encode     - Optional membrane_id for session boundary  OUTPUTS:     - FMLToken with all 9 layers:         L1: Basin        - Fernande",
        "k4": "FML Frequency Encoder Shell - Full 9-Layer Deterministic Token Generation HEX_ID: 0BF1DD10  Standalone version for cubesquare.  Converts any text input into a deterministic 9-layer CST token. Same inp",
        "k8": "FML Frequency Encoder Shell - Full 9-Layer Deterministic Token Generation HEX_ID"
      },
      "api_refs": []
    },
    "A13015B4": {
      "file_path": "cubesquare\\shells\\gene.py",
      "content_hash": 332930621515975028,
      "topics": [
        "cubesquare",
        "shells",
        "gene",
        "matrixidentity",
        "geneprofile",
        "geneshell",
        "to_dict",
        "morton_spread_bits",
        "morton_encode",
        "token_to_coords",
        "coords_to_hex_id",
        "is_palindrome",
        "get_matrix_identity",
        "get_token_identity",
        "breed_identities"
      ],
      "basin": 19,
      "layer": 2,
      "summaries": {
        "k0": "Gene Shell - CST Matrix Identity and Reproduction Engine ========================================================= Gene Model Shell for cubesquare_standalone.  This shell provides gene theory operations for the 48x48x48 Matrix system, including identity generation, breeding, and lineage tracking.  Commands:     status          - Show system status     generate        - Generate identity for a token string     breed           - Breed two identities     profile         - Get identity profile at co",
        "k4": "Gene Shell - CST Matrix Identity and Reproduction Engine ========================================================= Gene Model Shell for cubesquare_standalone.  This shell provides gene theory operatio",
        "k8": "Gene Shell - CST Matrix Identity and Reproduction Engine ======================="
      },
      "api_refs": []
    },
    "541051B5": {
      "file_path": "cubesquare\\shells\\gravity.py",
      "content_hash": 11192093130145538766,
      "topics": [
        "cubesquare",
        "shells",
        "gravity",
        "gravityshell",
        "hex_to_morton",
        "morton_decode_wrapped",
        "compute_k11_level",
        "compute_basin",
        "compute_mass_from_prime",
        "compute_distance",
        "is_prime"
      ],
      "basin": 65,
      "layer": 5,
      "summaries": {
        "k0": "Gravity Shell - Celestial Prime Validation & Orbital Mechanics ===============================================================  HEX_ID: 43208FA3 AREA: Physical (43) COMPONENT: Gravity (20) LEVEL: Shell (8F) INSTANCE: Quaternary (A3)  WORLD VALIDATION MODEL  Celestial Primes encode planetary positions and masses:     Earth Prime:   6584  (base reference)     Sun Prime:     2179  (central mass)     Moon Prime:    79    (orbital resonance)     Jupiter Prime: 2089  (outer reference)  Key Relationshi",
        "k4": "Gravity Shell - Celestial Prime Validation & Orbital Mechanics ===============================================================  HEX_ID: 43208FA3 AREA: Physical (43) COMPONENT: Gravity (20) LEVEL: Shel",
        "k8": "Gravity Shell - Celestial Prime Validation & Orbital Mechanics ================="
      },
      "api_refs": []
    },
    "32138CD2": {
      "file_path": "cubesquare\\shells\\i_logic.py",
      "content_hash": 17450668458033229722,
      "topics": [
        "cubesquare",
        "shells",
        "logic",
        "ilogicshell",
        "status",
        "multiply",
        "compose",
        "predict"
      ],
      "basin": 33,
      "layer": 3,
      "summaries": {
        "k0": "I-Logic Shell - I-Logic Operations Standalone version for cubesquare package.",
        "k4": "I-Logic Shell - I-Logic Operations Standalone version for cubesquare package.",
        "k8": "I-Logic Shell - I-Logic Operations Standalone version for cubesquare package."
      },
      "api_refs": []
    },
    "17928F49": {
      "file_path": "cubesquare\\shells\\language.py",
      "content_hash": 9721266736072389798,
      "topics": [
        "cubesquare",
        "shells",
        "language",
        "files",
        "acceptedidea",
        "languageshell"
      ],
      "basin": 121,
      "layer": 1,
      "summaries": {
        "k0": "Language Shell - Semantic Communication Layer Standalone version for cubesquare package.  HEX_ID: 4C414E47 (LANG)  Bridges machine ideas to human-readable language: - DATA (patterns) -> LANGUAGE (human-readable sentences) - IDEAS (machine) -> COMMUNICATION (visual + text) - I-Logic states -> VOCABULARY (word choice and tone)  Components:     1. SEMANTIC VOCABULARY - Word/phrase templates for each I-Logic state     2. IDEA TEMPLATES - Convert idea types to sentences     3. VISUAL MATRIX - Display",
        "k4": "Language Shell - Semantic Communication Layer Standalone version for cubesquare package.  HEX_ID: 4C414E47 (LANG)  Bridges machine ideas to human-readable language: - DATA (patterns) -> LANGUAGE (huma",
        "k8": "Language Shell - Semantic Communication Layer Standalone version for cubesquare "
      },
      "api_refs": []
    },
    "F5E0E3E4": {
      "file_path": "cubesquare\\shells\\learning.py",
      "content_hash": 8754557929793298363,
      "topics": [
        "cubesquare",
        "shells",
        "learning",
        "layersemantic",
        "srlsemanticmapping",
        "learningpattern",
        "generatedidea",
        "layersemanticloader",
        "srlsemanticbridge",
        "bidirectionallearning",
        "learningshell",
        "load_all"
      ],
      "basin": 94,
      "layer": 7,
      "summaries": {
        "k0": "Learning Shell - Layer Semantic Integration & Bidirectional Learning (Standalone) ================================================================================== HEX_ID: 4C524E47 (LRNG - Tools/Shell/Learning/Primary)  Standalone learning shell for the cubesquare package. Bridges documentation to runtime with layer semantic integration.  CG:HEX|V1|AGENT:4C524E47 MAP:L1=01F2,L2=02F3,L3=03F4,L4=04F5,L5=05F6,L6=06F7,L7=07F8,L8=08F9,L9=09F2 CMD:?L=query_layer,@L=ref_layer,+P=pattern,!I=idea MORTON",
        "k4": "Learning Shell - Layer Semantic Integration & Bidirectional Learning (Standalone) ================================================================================== HEX_ID: 4C524E47 (LRNG - Tools/Shel",
        "k8": "Learning Shell - Layer Semantic Integration & Bidirectional Learning (Standalone"
      },
      "api_refs": []
    },
    "F6331B2A": {
      "file_path": "cubesquare\\shells\\light.py",
      "content_hash": 8554684446470320242,
      "topics": [
        "cubesquare",
        "shells",
        "light",
        "lightshell",
        "c_to_light_units",
        "light_units_to_c",
        "basin_to_c",
        "basin_to_light_units",
        "c_to_basin",
        "light_units_to_basin",
        "basin_to_layer",
        "layer_to_basins",
        "c_to_layer_group",
        "c_to_ilogic"
      ],
      "basin": 99,
      "layer": 7,
      "summaries": {
        "k0": "Light Basin Shell - Unified Light Unit <-> Basin <-> Layer Mapping Standalone version for cubesquare package.  HEX_ID: 4C424153 (LBAS)  CLI interface for the Fernandez Light Unit coordinate system. The OCTA mapping for FML and core of each agent's spatial position.  CORE CALIBRATION:     sqrt(3) = 1 Light Unit (LU)     C = sqrt(3) = 1 LU (unit boundary)     c_abstract = 1/sqrt(3) = speed of light in Fernandez units  MAPPING:     C = 0       -> 0.00 LU -> L1-L3 (Geometric/Semantic/Spatial)    -> ",
        "k4": "Light Basin Shell - Unified Light Unit <-> Basin <-> Layer Mapping Standalone version for cubesquare package.  HEX_ID: 4C424153 (LBAS)  CLI interface for the Fernandez Light Unit coordinate system. Th",
        "k8": "Light Basin Shell - Unified Light Unit <-> Basin <-> Layer Mapping Standalone ve"
      },
      "api_refs": []
    },
    "87228F6F": {
      "file_path": "cubesquare\\shells\\manifold.py",
      "content_hash": 3353509934323219888,
      "topics": [
        "cubesquare",
        "shells",
        "manifold",
        "ilogicstate",
        "manifoldagent",
        "manifoldshell",
        "to_dict",
        "generate_hex_id",
        "generate_agent_for_need"
      ],
      "basin": 114,
      "layer": 1,
      "summaries": {
        "k0": "Manifold Shell - The Square: Manifold-Content-Surface-Observation =================================================================== Manifold Shell for cubesquare_standalone.  This shell implements the manifold system where: - Manifold defines what can be observed - Observation defines the manifold's surface - Neither exists without the other (mutual definition) - This IS self-identity  Commands:     status          - Full system status     agents          - List agents with I-Logic states     ",
        "k4": "Manifold Shell - The Square: Manifold-Content-Surface-Observation =================================================================== Manifold Shell for cubesquare_standalone.  This shell implements t",
        "k8": "Manifold Shell - The Square: Manifold-Content-Surface-Observation =============="
      },
      "api_refs": []
    },
    "E5138ED2": {
      "file_path": "cubesquare\\shells\\mass.py",
      "content_hash": 3846869426546230192,
      "topics": [
        "cubesquare",
        "shells",
        "mass",
        "massshell",
        "hex_to_morton",
        "morton_decode_wrapped",
        "compute_k11_level",
        "compute_phi_norm",
        "compute_mass",
        "compute_em_coupling",
        "compute_energy_equivalent",
        "get_token_mass"
      ],
      "basin": 81,
      "layer": 6,
      "summaries": {
        "k0": "Mass Shell - K11 Mass Coupling for CST Tokens ==============================================  HEX_ID: 43208FA2 AREA: Physical (43) COMPONENT: Mass (20) LEVEL: Shell (8F) INSTANCE: Tertiary (A2)  Core Principle: mass = K11 * (1 + k11_level / 11) Mass emerges from the K11 hendecagonal constant coupled with position in the manifold. EM coupling = K5 * K11 * phi_norm gives the electromagnetic mass equivalent.  Celestial Mass Primes:     Sun Prime: 2179 (central mass reference)     Earth Prime: 6584 ",
        "k4": "Mass Shell - K11 Mass Coupling for CST Tokens ==============================================  HEX_ID: 43208FA2 AREA: Physical (43) COMPONENT: Mass (20) LEVEL: Shell (8F) INSTANCE: Tertiary (A2)  Core ",
        "k8": "Mass Shell - K11 Mass Coupling for CST Tokens =================================="
      },
      "api_refs": []
    },
    "53F3897D": {
      "file_path": "cubesquare\\shells\\meaning.py",
      "content_hash": 9761953281701723815,
      "topics": [
        "cubesquare",
        "shells",
        "meaning",
        "meaningshell"
      ],
      "basin": 63,
      "layer": 5,
      "summaries": {
        "k0": "Meaning Shell - Self-Reference and Semantic Access for Agents ============================================================== Meaning Shell for cubesquare_standalone.  This shell provides semantic meaning and self-reference operations: - Basin semantic lookup (131 basins, 9 layers, 5 I-Logic states) - Self-reference operations (P-P=0, P/P=1) - Agent contextualization - 12-layer navigation - K11 fractal positioning  All meaning happens INSIDE the unit. Agents use this to understand their own meani",
        "k4": "Meaning Shell - Self-Reference and Semantic Access for Agents ============================================================== Meaning Shell for cubesquare_standalone.  This shell provides semantic mean",
        "k8": "Meaning Shell - Self-Reference and Semantic Access for Agents =================="
      },
      "api_refs": []
    },
    "75A31965": {
      "file_path": "cubesquare\\shells\\performance.py",
      "content_hash": 9544631584673275614,
      "topics": [
        "cubesquare",
        "shells",
        "performance",
        "performanceshell",
        "status",
        "benchmark",
        "test",
        "run"
      ],
      "basin": 90,
      "layer": 7,
      "summaries": {
        "k0": "Performance Shell - C Backend Tests (with Python fallback) Standalone version for cubesquare package.",
        "k4": "Performance Shell - C Backend Tests (with Python fallback) Standalone version for cubesquare package.",
        "k8": "Performance Shell - C Backend Tests (with Python fallback) Standalone version fo"
      },
      "api_refs": []
    },
    "E4A08088": {
      "file_path": "cubesquare\\shells\\predict.py",
      "content_hash": 3257447146696439903,
      "topics": [
        "cubesquare",
        "shells",
        "predict",
        "predictshell",
        "status",
        "route",
        "resolve",
        "cycle"
      ],
      "basin": 74,
      "layer": 6,
      "summaries": {
        "k0": "Predict Shell - Route Prediction Standalone version for cubesquare package.",
        "k4": "Predict Shell - Route Prediction Standalone version for cubesquare package.",
        "k8": "Predict Shell - Route Prediction Standalone version for cubesquare package."
      },
      "api_refs": []
    },
    "E5638E76": {
      "file_path": "cubesquare\\shells\\primitives.py",
      "content_hash": 9160676744610671072,
      "topics": [
        "cubesquare",
        "shells",
        "primitives",
        "primitivesshell",
        "status",
        "morton_encode",
        "basin",
        "srl",
        "i_logic",
        "use"
      ],
      "basin": 86,
      "layer": 6,
      "summaries": {
        "k0": "Primitives Shell - Verified O(1) Primitives Standalone version for cubesquare package.",
        "k4": "Primitives Shell - Verified O(1) Primitives Standalone version for cubesquare package.",
        "k8": "Primitives Shell - Verified O(1) Primitives Standalone version for cubesquare pa"
      },
      "api_refs": []
    },
    "90A232E2": {
      "file_path": "cubesquare\\shells\\semantic.py",
      "content_hash": 7096924227435617732,
      "topics": [
        "cubesquare",
        "shells",
        "semantic",
        "l2class",
        "predicatetype",
        "encodedcondition",
        "primitive",
        "relationship",
        "parseresult",
        "agentmatch",
        "routingplan",
        "semanticshell",
        "to_dict"
      ],
      "basin": 10,
      "layer": 1,
      "summaries": {
        "k0": "Semantic Chain Shell - Language to Geometry Decomposition Standalone version for cubesquare package.  HEX_ID: 53454D43 (SEMC)  Decomposes natural language into geometric primitives using frequency-based basin mapping and I-Logic state routing. This is DECOMPOSITION not TRANSLATION.  Components (embedded): - Basin Dictionary: Maps terms to basins via frequency (Zipf's law) - Condition Encoder: Creates ephemeral tokens with I-Logic states - FML Sentence Parser: Decomposes language into primitives ",
        "k4": "Semantic Chain Shell - Language to Geometry Decomposition Standalone version for cubesquare package.  HEX_ID: 53454D43 (SEMC)  Decomposes natural language into geometric primitives using frequency-bas",
        "k8": "Semantic Chain Shell - Language to Geometry Decomposition Standalone version for"
      },
      "api_refs": []
    },
    "C2D2A669": {
      "file_path": "cubesquare\\shells\\sql.py",
      "content_hash": 17431324626684478341,
      "topics": [
        "cubesquare",
        "shells",
        "sql",
        "operationtype",
        "operationmetrics",
        "sqlshell",
        "duration_ms",
        "to_dict"
      ],
      "basin": 45,
      "layer": 4,
      "summaries": {
        "k0": "SQL Shell - Database Operations with CST Awareness (Standalone) ================================================================ HEX_ID: 53514C00 (SQL) AREA: SQL Operations (53) COMPONENT: Shell Interface (51) LEVEL: Core (4C) INSTANCE: Primary (00)  Standalone SQL shell for the cubesquare package. Provides database operations with CST integration awareness.  ================================================================================ CRITICAL ARCHITECTURAL DISTINCTION ======================",
        "k4": "SQL Shell - Database Operations with CST Awareness (Standalone) ================================================================ HEX_ID: 53514C00 (SQL) AREA: SQL Operations (53) COMPONENT: Shell Inter",
        "k8": "SQL Shell - Database Operations with CST Awareness (Standalone) ================"
      },
      "api_refs": []
    },
    "C372AAEB": {
      "file_path": "cubesquare\\shells\\srl.py",
      "content_hash": 6183400168948079121,
      "topics": [
        "cubesquare",
        "shells",
        "srl",
        "cunifiedresult",
        "srlpathresult",
        "srlbatchresult",
        "srlagentcontext",
        "srlvoxelcontext",
        "srlqrscontext",
        "srlshell"
      ],
      "basin": 55,
      "layer": 4,
      "summaries": {
        "k0": "SRL Shell - Square Root Loop Entry Point (Standalone) ====================================================== HEX_ID: 00F20500  Standalone version of the SRL (Square Root Loop) system with O(1) pathfinding. SRL Shell for cubesquare_standalone.  Mathematical Foundation:     t = d/t -> t^2 = d -> t = sqrt(d)      The loop is INSIDE the unit (self-reference), not external iteration.     This enables O(1) instant path computation without BFS traversal.  Four-State System:     State I   (i=1):   DIREC",
        "k4": "SRL Shell - Square Root Loop Entry Point (Standalone) ====================================================== HEX_ID: 00F20500  Standalone version of the SRL (Square Root Loop) system with O(1) pathfin",
        "k8": "SRL Shell - Square Root Loop Entry Point (Standalone) =========================="
      },
      "api_refs": []
    },
    "867386FB": {
      "file_path": "cubesquare\\shells\\telemetry.py",
      "content_hash": 14194095068001847904,
      "topics": [
        "cubesquare",
        "shells",
        "telemetry",
        "srlstate",
        "telemetryeventtype",
        "telemetryevent",
        "agenttelemetry",
        "messageinterpreter",
        "anomalydetector",
        "statepredictor",
        "semanticrouter",
        "telemetryshell",
        "i_value",
        "state_name",
        "vector",
        "description",
        "to_dict"
      ],
      "basin": 103,
      "layer": 1,
      "summaries": {
        "k0": "Telemetry Shell - Agent Telemetry and State Prediction HEX_ID: 50483354 (PH3T - Telemetry)  PURE PYTHON VERSION - NO OLLAMA, NO LLM DEPENDENCIES  This is a standalone telemetry shell that provides: - Pattern-based message interpretation - Anomaly detection - State prediction via SRL trajectory - Semantic routing  INPUTS:     - Natural language messages     - Hex IDs (8-char strings)     - Agent coordinates (x, y, z in 0-47)     - Basin numbers (0-130)     - K11 levels (-11 to +11)     - I-Logic ",
        "k4": "Telemetry Shell - Agent Telemetry and State Prediction HEX_ID: 50483354 (PH3T - Telemetry)  PURE PYTHON VERSION - NO OLLAMA, NO LLM DEPENDENCIES  This is a standalone telemetry shell that provides: - ",
        "k8": "Telemetry Shell - Agent Telemetry and State Prediction HEX_ID: 50483354 (PH3T - "
      },
      "api_refs": []
    },
    "903018AE": {
      "file_path": "cubesquare\\shells\\thinking.py",
      "content_hash": 18328177231630537778,
      "topics": [
        "cubesquare",
        "shells",
        "thinking",
        "thinkingstep",
        "thinkingcycle",
        "agentmatch",
        "autonomousagent",
        "thinkingshell",
        "to_dict"
      ],
      "basin": 3,
      "layer": 1,
      "summaries": {
        "k0": "Thinking Shell - Autonomous Agent Loop with Geometric I-Logic Standalone version for cubesquare package.  HEX_ID: 5448494B (THINK)  CLI wrapper for autonomous agent thinking. Agents think using GEOMETRIC decomposition, not keywords.  Thinking Phases:     OBSERVE   - Perceive current state from environment     DECOMPOSE - Break down observations into primitives     REASON    - Apply I-Logic multiplication for routing     ACT       - Execute chosen action     REFLECT   - Evaluate outcome and updat",
        "k4": "Thinking Shell - Autonomous Agent Loop with Geometric I-Logic Standalone version for cubesquare package.  HEX_ID: 5448494B (THINK)  CLI wrapper for autonomous agent thinking. Agents think using GEOMET",
        "k8": "Thinking Shell - Autonomous Agent Loop with Geometric I-Logic Standalone version"
      },
      "api_refs": []
    },
    "437383DD": {
      "file_path": "cubesquare\\shells\\time.py",
      "content_hash": 9099057960353395105,
      "topics": [
        "cubesquare",
        "shells",
        "time",
        "timeshell",
        "hex_to_morton",
        "morton_decode_wrapped",
        "time_from_distance",
        "distance_from_time",
        "compute_phase",
        "compute_position",
        "compute_velocity",
        "time_dilation",
        "get_srl_state",
        "get_token_time_sta"
      ],
      "basin": 55,
      "layer": 4,
      "summaries": {
        "k0": "Time Shell - Temporal Operations for CST Units ===============================================  HEX_ID: 43208FA0 AREA: Physical (43) COMPONENT: Time (20) LEVEL: Shell (8F) INSTANCE: Primary (A0)  Core Principle: t = d/t -> t = sqrt(d) Time is computed O(1) from distance. The observer samples; the state exists at all t.  Celestial Integration:     Earth Prime: 6584 (base reference)     21/80 ratio: Sun gravitational influence     20/79 ratio: Jupiter-Moon coupling  Commands:     status      - Tim",
        "k4": "Time Shell - Temporal Operations for CST Units ===============================================  HEX_ID: 43208FA0 AREA: Physical (43) COMPONENT: Time (20) LEVEL: Shell (8F) INSTANCE: Primary (A0)  Core",
        "k8": "Time Shell - Temporal Operations for CST Units ================================="
      },
      "api_refs": []
    },
    "D453822E": {
      "file_path": "cubesquare\\shells\\twelve.py",
      "content_hash": 3232317262921471928,
      "topics": [
        "cubesquare",
        "shells",
        "twelve",
        "ilogicstate",
        "layer",
        "l1",
        "l2",
        "l3",
        "l4",
        "l5",
        "l6",
        "l7",
        "l8",
        "l9",
        "l10",
        "l11",
        "l12",
        "tokenunit",
        "twelvelayermanifold",
        "twelveshell"
      ],
      "basin": 69,
      "layer": 5,
      "summaries": {
        "k0": "Twelve Layer Manifold - Complete Token Unit Architecture (Standalone) ====================================================================== HEX_ID: 12LAYER00 AREA: Manifold (12) COMPONENT: Full Layer System (LA) VERSION: 1.0  Standalone twelve-layer manifold shell for the cubesquare package. Each token is a UNIT with full logic at their disposition across all 12 layers.  LAYERS: ------- INTERNAL (Inside Membrane):     L1  GEOMETRIC         - Shape, structure, form     L2  SEMANTIC          - Me",
        "k4": "Twelve Layer Manifold - Complete Token Unit Architecture (Standalone) ====================================================================== HEX_ID: 12LAYER00 AREA: Manifold (12) COMPONENT: Full Layer",
        "k8": "Twelve Layer Manifold - Complete Token Unit Architecture (Standalone) =========="
      },
      "api_refs": []
    },
    "86D38ADD": {
      "file_path": "cubesquare\\shells\\unified.py",
      "content_hash": 10741176522130857521,
      "topics": [
        "cubesquare",
        "shells",
        "unified",
        "ilogicstate",
        "thinkingstate",
        "unifiedshell",
        "morton_spread_bits",
        "morton_compact_bits",
        "morton_encode",
        "morton_decode",
        "hex_to_morton",
        "classify_layer",
        "ilogic_multiply"
      ],
      "basin": 109,
      "layer": 1,
      "summaries": {
        "k0": "Unified Field Shell - Agent Thinking Protocols and Self-Preservation ===================================================================== Unified Field Shell for cubesquare_standalone.  This shell provides the unified field tools for agents: - Token extraction and recovery - Code generation from tokens - Coherence-based healing - Gap detection and patching - Layer-based tool creation - Self-modification analysis  Commands:     status          - Show system status     extract         - Extract t",
        "k4": "Unified Field Shell - Agent Thinking Protocols and Self-Preservation ===================================================================== Unified Field Shell for cubesquare_standalone.  This shell pr",
        "k8": "Unified Field Shell - Agent Thinking Protocols and Self-Preservation ==========="
      },
      "api_refs": []
    },
    "97C017A3": {
      "file_path": "cubesquare\\shells\\validation.py",
      "content_hash": 4183590639929457602,
      "topics": [
        "cubesquare",
        "shells",
        "validation",
        "validationresult",
        "validationresults",
        "validationshell",
        "to_dict",
        "add",
        "passed_count",
        "failed_count",
        "get_summary",
        "print_summary"
      ],
      "basin": 124,
      "layer": 1,
      "summaries": {
        "k0": "Validation Shell - Agent and System Validation (Standalone) ============================================================ HEX_ID: F6F40F40 AREA: Tools/Agents (F6) COMPONENT: Validation Shell (F4) LEVEL: Root level (0F) INSTANCE: New Agent Validation (40)  Standalone validation shell for the cubesquare package. Comprehensive validation tool for agent shell ecosystem.  Tests all integration points: - SRL Shell (O(1) pathfinding) - CST Shell (5-layer tokenization) - C Backend (sub-nanosecond operati",
        "k4": "Validation Shell - Agent and System Validation (Standalone) ============================================================ HEX_ID: F6F40F40 AREA: Tools/Agents (F6) COMPONENT: Validation Shell (F4) LEVEL",
        "k8": "Validation Shell - Agent and System Validation (Standalone) ===================="
      },
      "api_refs": []
    },
    "75823DE7": {
      "file_path": "cubesquare\\shells\\world.py",
      "content_hash": 16423983928168463707,
      "topics": [
        "cubesquare",
        "shells",
        "world",
        "worldshell",
        "morton_decode"
      ],
      "basin": 88,
      "layer": 7,
      "summaries": {
        "k0": "World Shell - Complete Physical Universe Interface (Standalone) ================================================================ HEX_ID: 43208FA4  Standalone version of the physical universe interface shell. World Shell for cubesquare_standalone.  This shell unifies time, distance, mass, and gravity into a complete physical universe. Every token exists as a body with all physical properties.  The universe validates itself against the solar system:     - Earth (6584): Reference frame, INVERSE, re",
        "k4": "World Shell - Complete Physical Universe Interface (Standalone) ================================================================ HEX_ID: 43208FA4  Standalone version of the physical universe interface",
        "k8": "World Shell - Complete Physical Universe Interface (Standalone) ================"
      },
      "api_refs": []
    },
    "32B23F49": {
      "file_path": "cubesquare\\shells\\beehive.py",
      "content_hash": 14557689526434385396,
      "topics": [
        "cubesquare",
        "shells",
        "beehive",
        "beehiveshell",
        "status"
      ],
      "basin": 43,
      "layer": 3,
      "summaries": {
        "k0": "Beehive Shell - Token Index Operations (CST-Native) Standalone version for cubesquare package.  Reads from beehive_index.cst (binary, 601KB) NOT beehive_index.json (37MB).  CST Binary Format:     Header (24 bytes):         - Magic: \"CST\\x00\" (4 bytes)         - Version: uint32 (4 bytes)         - Token count: uint32 (4 bytes)         - Queen hex: 8 bytes         - Reserved: 4 bytes      Tokens (25 bytes each):         - Morton code: uint64 (8 bytes)         - Hex ID: 8 bytes ASCII         - Basi",
        "k4": "Beehive Shell - Token Index Operations (CST-Native) Standalone version for cubesquare package.  Reads from beehive_index.cst (binary, 601KB) NOT beehive_index.json (37MB).  CST Binary Format:     Head",
        "k8": "Beehive Shell - Token Index Operations (CST-Native) Standalone version for cubes"
      },
      "api_refs": []
    },
    "32A0545E": {
      "file_path": "cubesquare\\shells\\phi.py",
      "content_hash": 2994787741643713777,
      "topics": [
        "cubesquare",
        "shells",
        "phi",
        "cstlayer",
        "layerllmresult",
        "agentcontext",
        "councilvote",
        "layerllmprocessor",
        "agentllmcommunicator",
        "observercouncilllm",
        "phishell",
        "level",
        "layer_name",
        "llm_role",
        "detect_i_logic_from_text",
        "calculate_coherence"
      ],
      "basin": 42,
      "layer": 3,
      "summaries": {
        "k0": "PhiShell - LLM Integration with CST Structure Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO dependencies on pipe_v001, CreatureGarage, or hou.  Deep integration connecting Ollama (phi4/phi4-mini) to 9 CST layers. Each layer has semantic processing via LLM with graceful fallback.  Requirements (optional):     pip install ollama     ollama pull phi4-mini  # or phi4 for full reasoning",
        "k4": "PhiShell - LLM Integration with CST Structure Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO dependencies on pipe_v001",
        "k8": "PhiShell - LLM Integration with CST Structure Standalone version for cubesquare "
      },
      "api_refs": []
    },
    "06C28DAF": {
      "file_path": "cubesquare\\shells\\ogawa.py",
      "content_hash": 5700854767221048937,
      "topics": [
        "cubesquare",
        "shells",
        "ogawa",
        "vec3f",
        "vec2f",
        "box3f",
        "facetopology",
        "uvset",
        "tangentframe",
        "manifold",
        "polymesh",
        "archive",
        "cstmeshheader",
        "cstmesh",
        "ogawashell"
      ],
      "basin": 108,
      "layer": 1,
      "summaries": {
        "k0": "OgawaShell - Alembic/Ogawa Mesh Parser with CST Binary Format Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO dependencies on pipe_v001, CreatureGarage, or hou.  Exposes cst_unit.dll Ogawa functions via MCP-compatible interface. CST binary format provides O(1) mmap loading with Morton-encoded spatial indices.  Note: ABC parsing requires cst_unit.dll with ogawa_* functions.       CST binary read/write works independe",
        "k4": "OgawaShell - Alembic/Ogawa Mesh Parser with CST Binary Format Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO dependenc",
        "k8": "OgawaShell - Alembic/Ogawa Mesh Parser with CST Binary Format Standalone version"
      },
      "api_refs": []
    },
    "31F1175C": {
      "file_path": "cubesquare\\shells\\vision.py",
      "content_hash": 732878065987920182,
      "topics": [
        "cubesquare",
        "shells",
        "vision",
        "skycolor",
        "sunposition",
        "rayresult",
        "visionshell",
        "wavelength_to_basin",
        "basin_to_wavelength",
        "wavelength_to_rgb",
        "hex_to_coords",
        "coords_to_elevation_azimuth",
        "rayleigh_scatter"
      ],
      "basin": 31,
      "layer": 3,
      "summaries": {
        "k0": "VisionShell - Agent Physics Vision Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO dependencies on pipe_v001, CreatureGarage, or hou.  Physics vision calculations using CST constants:     - Sky dome: hex \u2192 morton \u2192 coords \u2192 sky color     - Sun position: hex \u2192 coords \u2192 orbital mechanics     - Ray tracing: wavelength \u2192 basin (L7), direction \u2192 morton path     - Camera simulation",
        "k4": "VisionShell - Agent Physics Vision Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO dependencies on pipe_v001, CreatureG",
        "k8": "VisionShell - Agent Physics Vision Standalone version for cubesquare package.  N"
      },
      "api_refs": []
    },
    "53C38B59": {
      "file_path": "cubesquare\\shells\\copilot.py",
      "content_hash": 9080909726300611315,
      "topics": [
        "cubesquare",
        "shells",
        "copilot",
        "copilotshell",
        "phi_compression_ratio",
        "diagonal_mapping",
        "membrane_architecture",
        "freq_to_emotion"
      ],
      "basin": 60,
      "layer": 5,
      "summaries": {
        "k0": "CopilotShell - Master Utility Router Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO dependencies on pipe_v001, CreatureGarage, or hou.  Cherry-picked self-contained operations from CG copilot:     - System status via existing shells     - Diagonal mapping (sqrt(2)/sqrt(3))     - PHI compression formula     - Membrane architecture (pi-phi-F)     - Musical/emotional frequency spectrum     - Beats-emotions mapping (11",
        "k4": "CopilotShell - Master Utility Router Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO dependencies on pipe_v001, Creatur",
        "k8": "CopilotShell - Master Utility Router Standalone version for cubesquare package. "
      },
      "api_refs": []
    },
    "86B30654": {
      "file_path": "cubesquare\\shells\\__init__.py",
      "content_hash": 3095529839557228613,
      "topics": [
        "cubesquare",
        "shells"
      ],
      "basin": 107,
      "layer": 1,
      "summaries": {
        "k0": "Cubesquare Shells - Core Shell Implementations =============================================== Standalone versions with refactored imports.  Core Shells:     CSTShell        - CST 9-layer operations     ILogicShell     - I-Logic 4-state system     CircularShell   - Circular validation and K11     PrimitivesShell - Verified primitives (Morton, Basin, SRL, I-Logic)     PredictShell    - Route prediction via I-Logic     BeehiveShell    - Beehive clustering     PerformanceShell - C backend performan",
        "k4": "Cubesquare Shells - Core Shell Implementations =============================================== Standalone versions with refactored imports.  Core Shells:     CSTShell        - CST 9-layer operations  ",
        "k8": "Cubesquare Shells - Core Shell Implementations ================================="
      },
      "api_refs": []
    },
    "75A08903": {
      "file_path": "cubesquare\\shells\\chat.py",
      "content_hash": 13164543190299317935,
      "topics": [
        "cubesquare",
        "shells",
        "chat",
        "chatmessage",
        "chatresponse",
        "conversationstate",
        "chatshell",
        "compute_message_hash",
        "content_to_hex_id",
        "detect_i_logic_state",
        "add_message"
      ],
      "basin": 90,
      "layer": 7,
      "summaries": {
        "k0": "ChatShell - Bidirectional Chat Interface with Hex Tracking Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO dependencies on pipe_v001, CreatureGarage, or hou.  Routes messages through:     - Semantic decomposition -> Layer routing -> I-Logic prediction     - Hex identity tracking for each message     - Circular loop detection to prevent infinite agent loops",
        "k4": "ChatShell - Bidirectional Chat Interface with Hex Tracking Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO dependencies",
        "k8": "ChatShell - Bidirectional Chat Interface with Hex Tracking Standalone version fo"
      },
      "api_refs": []
    },
    "8710086F": {
      "file_path": "cubesquare\\shells\\content.py",
      "content_hash": 14900120277044188208,
      "topics": [
        "cubesquare",
        "shells",
        "content",
        "hexidentity",
        "contenttoken",
        "queryresult",
        "hexcommunicator",
        "contentcstindex",
        "contentshell",
        "compute_topic_hash",
        "compute_basin",
        "compute_layer",
        "topic_to_hex_identity"
      ],
      "basin": 113,
      "layer": 1,
      "summaries": {
        "k0": "ContentShell - Hex Identity Tokenization and Documentation Index Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO dependencies on pipe_v001, CreatureGarage, or hou.  HEX IDENTITY PROTOCOL:     - Each topic/content maps to 8-char hex ID     - Hex encodes: Morton (20 bits) + Basin (8 bits) + Layer (3 bits) + I-state (1 bit)     - Bidirectional: encode topic -> hex, decode hex -> components  TOKEN SAVINGS:     Tradition",
        "k4": "ContentShell - Hex Identity Tokenization and Documentation Index Standalone version for cubesquare package.  NO Python for-loops in hot paths. ALL batch operations use C backend via _core. ZERO depend",
        "k8": "ContentShell - Hex Identity Tokenization and Documentation Index Standalone vers"
      },
      "api_refs": []
    },
    "7602102C": {
      "file_path": "cubesquare\\_core\\constants.py",
      "content_hash": 16811642055104939462,
      "topics": [
        "cubesquare",
        "core",
        "constants"
      ],
      "basin": 96,
      "layer": 7,
      "summaries": {
        "k0": "Cubesquare Constants  Mathematical constants that define the CST system.",
        "k4": "Cubesquare Constants  Mathematical constants that define the CST system.",
        "k8": "Cubesquare Constants  Mathematical constants that define the CST system."
      },
      "api_refs": []
    },
    "E5203884": {
      "file_path": "cubesquare\\_core\\morton.py",
      "content_hash": 12252301988515805181,
      "topics": [
        "cubesquare",
        "core",
        "morton",
        "encoding",
        "order",
        "space",
        "filling",
        "curve",
        "encode",
        "decode",
        "encode_2d",
        "decode_2d",
        "batch_encode",
        "batch_decode",
        "distance",
        "neighbors"
      ],
      "basin": 82,
      "layer": 6,
      "summaries": {
        "k0": "Morton Encoding - O(1) Z-order Space-Filling Curve  Pure Python implementation with optional numpy acceleration.",
        "k4": "Morton Encoding - O(1) Z-order Space-Filling Curve  Pure Python implementation with optional numpy acceleration.",
        "k8": "Morton Encoding - O(1) Z-order Space-Filling Curve  Pure Python implementation w"
      },
      "api_refs": []
    },
    "979155F2": {
      "file_path": "cubesquare\\_core\\__init__.py",
      "content_hash": 17617778300061377394,
      "topics": [
        "cubesquare",
        "core",
        "backend",
        "with",
        "pure",
        "python",
        "fallback",
        "centryresult",
        "morton_encode"
      ],
      "basin": 121,
      "layer": 1,
      "summaries": {
        "k0": "Cubesquare Core - C Backend with Pure Python Fallback  Performance Operations (via c_entry_orchestrator.dll): - Morton Encode:     0.009 ns (FASTEST) - AVX2 SIMD:         0.291 ns - CST Morton PDEP:   1.03 ns - SRL Diagonal:      1.280 ns - Fernandez O(1):    1.99 ns - CST Combined:      6.30 ns  Falls back to pure Python if DLL unavailable.",
        "k4": "Cubesquare Core - C Backend with Pure Python Fallback  Performance Operations (via c_entry_orchestrator.dll): - Morton Encode:     0.009 ns (FASTEST) - AVX2 SIMD:         0.291 ns - CST Morton PDEP:  ",
        "k8": "Cubesquare Core - C Backend with Pure Python Fallback  Performance Operations (v"
      },
      "api_refs": []
    },
    "06A187DF": {
      "file_path": "cubesquare\\mcp\\transport.py",
      "content_hash": 7064647475610534137,
      "topics": [
        "cubesquare",
        "mcp",
        "transport",
        "layer",
        "stdiotransport",
        "directtransport",
        "set_handler",
        "start",
        "stop",
        "call",
        "call_tool"
      ],
      "basin": 106,
      "layer": 1,
      "summaries": {
        "k0": "MCP Transport Layer  Implements stdio transport for JSON-RPC 2.0 communication.",
        "k4": "MCP Transport Layer  Implements stdio transport for JSON-RPC 2.0 communication.",
        "k8": "MCP Transport Layer  Implements stdio transport for JSON-RPC 2.0 communication."
      },
      "api_refs": []
    },
    "17A1CFDB": {
      "file_path": "cubesquare\\mcp\\tools.py",
      "content_hash": 2964296797124334672,
      "topics": [
        "cubesquare",
        "mcp",
        "tools",
        "tool",
        "registry",
        "toolregistry"
      ],
      "basin": 122,
      "layer": 1,
      "summaries": {
        "k0": "MCP Tool Registry  Maps 33 MCP tools to cubesquare shell implementations. Each tool wraps a shell class and exposes its commands.",
        "k4": "MCP Tool Registry  Maps 33 MCP tools to cubesquare shell implementations. Each tool wraps a shell class and exposes its commands.",
        "k8": "MCP Tool Registry  Maps 33 MCP tools to cubesquare shell implementations. Each t"
      },
      "api_refs": []
    },
    "17E1CFB7": {
      "file_path": "cubesquare\\mcp\\server.py",
      "content_hash": 17039362980540594947,
      "topics": [
        "cubesquare",
        "mcp",
        "server",
        "implementation",
        "mcpserver",
        "run",
        "get_direct_transport",
        "list_tools",
        "call_tool",
        "get_tool_info",
        "main"
      ],
      "basin": 126,
      "layer": 1,
      "summaries": {
        "k0": "MCP Server Implementation  JSON-RPC 2.0 server for Model Context Protocol. Exposes 33 cubesquare tools to MCP clients.",
        "k4": "MCP Server Implementation  JSON-RPC 2.0 server for Model Context Protocol. Exposes 33 cubesquare tools to MCP clients.",
        "k8": "MCP Server Implementation  JSON-RPC 2.0 server for Model Context Protocol. Expos"
      },
      "api_refs": []
    },
    "75E0EB79": {
      "file_path": "cubesquare\\mcp\\__main__.py",
      "content_hash": 9264369889856176411,
      "topics": [
        "cubesquare",
        "mcp",
        "main",
        "entry",
        "point",
        "running",
        "server",
        "module",
        "print_tools",
        "test_tools",
        "call_tool"
      ],
      "basin": 94,
      "layer": 7,
      "summaries": {
        "k0": "Entry point for running MCP server as module.  Usage:     python -m cubesquare.mcp              # Run server (stdio)     python -m cubesquare.mcp --list       # List all tools     python -m cubesquare.mcp --test       # Run test suite     python -m cubesquare.mcp --call TOOL  # Call a tool",
        "k4": "Entry point for running MCP server as module.  Usage:     python -m cubesquare.mcp              # Run server (stdio)     python -m cubesquare.mcp --list       # List all tools     python -m cubesquare",
        "k8": "Entry point for running MCP server as module.  Usage:     python -m cubesquare.m"
      },
      "api_refs": []
    },
    "07318095": {
      "file_path": "cubesquare\\mcp\\__init__.py",
      "content_hash": 5911983885303612028,
      "topics": [
        "cubesquare",
        "mcp",
        "server"
      ],
      "basin": 115,
      "layer": 1,
      "summaries": {
        "k0": "Cubesquare MCP Server  Exposes 33 CST tools via Model Context Protocol (MCP). Enables Claude Desktop, Cursor, and other MCP clients to access the deterministic computational substrate.  Usage:     python -m cubesquare.mcp                    # Run server (stdio)     cubesquare mcp                              # Run via CLI     cubesquare mcp --list                       # List all tools     cubesquare mcp --test cst_shell status      # Test a tool  Protocol:     JSON-RPC 2.0 over stdio (stdin/std",
        "k4": "Cubesquare MCP Server  Exposes 33 CST tools via Model Context Protocol (MCP). Enables Claude Desktop, Cursor, and other MCP clients to access the deterministic computational substrate.  Usage:     pyt",
        "k8": "Cubesquare MCP Server  Exposes 33 CST tools via Model Context Protocol (MCP). En"
      },
      "api_refs": []
    },
    "A1C02B50": {
      "file_path": "examples\\quickstart.py",
      "content_hash": 1473262252195559523,
      "topics": [
        "examples",
        "quickstart",
        "cubesquare",
        "example",
        "main"
      ],
      "basin": 28,
      "layer": 2,
      "summaries": {
        "k0": "Cubesquare Quickstart Example  This example demonstrates the basic usage of cubesquare.",
        "k4": "Cubesquare Quickstart Example  This example demonstrates the basic usage of cubesquare.",
        "k8": "Cubesquare Quickstart Example  This example demonstrates the basic usage of cube"
      },
      "api_refs": []
    },
    "65403296": {
      "file_path": "examples\\semantic_routing.py",
      "content_hash": 9143877927094360844,
      "topics": [
        "examples",
        "semantic",
        "routing",
        "with",
        "logic",
        "main"
      ],
      "basin": 84,
      "layer": 6,
      "summaries": {
        "k0": "Semantic Routing with I-Logic  This example demonstrates how to use I-Logic for predicting routing outcomes in agent systems.",
        "k4": "Semantic Routing with I-Logic  This example demonstrates how to use I-Logic for predicting routing outcomes in agent systems.",
        "k8": "Semantic Routing with I-Logic  This example demonstrates how to use I-Logic for "
      },
      "api_refs": []
    },
    "C2D2AA55": {
      "file_path": "examples\\rag_vs_cst_comparison.py",
      "content_hash": 15612239496567346017,
      "topics": [
        "examples",
        "rag",
        "cst",
        "comparison",
        "cubesquare",
        "succeeds",
        "where",
        "fails",
        "print_header",
        "verify_c_backend",
        "simulate_rag_behavior",
        "demonstrate_cst_solution"
      ],
      "basin": 45,
      "layer": 4,
      "summaries": {
        "k0": "RAG vs CST Comparison - Why Cubesquare Succeeds Where RAG Fails  This example demonstrates the fundamental differences between: - RAG (Retrieval-Augmented Generation) with embeddings - CST (Cubesquare Semantic Technology) with deterministic coordinates  CRITICAL: NO PYTHON LOOPS IN HOT PATH All batch operations use C backend directly.  Run with: python examples/rag_vs_cst_comparison.py",
        "k4": "RAG vs CST Comparison - Why Cubesquare Succeeds Where RAG Fails  This example demonstrates the fundamental differences between: - RAG (Retrieval-Augmented Generation) with embeddings - CST (Cubesquare",
        "k8": "RAG vs CST Comparison - Why Cubesquare Succeeds Where RAG Fails  This example de"
      },
      "api_refs": []
    },
    "B1E15C12": {
      "file_path": "examples\\srl_locality_validation.py",
      "content_hash": 12332478870999429071,
      "topics": [
        "examples",
        "srl",
        "locality",
        "validation",
        "loop",
        "structure",
        "print_section",
        "demonstrate_srl_formula",
        "demonstrate_locality",
        "demonstrate_f_times_fi"
      ],
      "basin": 30,
      "layer": 3,
      "summaries": {
        "k0": "SRL Locality Validation - The Loop IS The Structure  CRITICAL INSIGHT FOR AGENTS: ============================ t = d/t  ->  t^2 = d  ->  t = sqrtd  This is NOT a loop you iterate over. This IS the loop - you're INSIDE it.  The formula f x f_i = d x t means: - f: function (Morton encode) - f_i: I-Logic state (direction) - d: depth (distance in coordinate space) - t: time (sqrtd - collapsed iterations)  LOCALITY: You are always inside the Fernandez unit sphere. The loop contains you - you don't co",
        "k4": "SRL Locality Validation - The Loop IS The Structure  CRITICAL INSIGHT FOR AGENTS: ============================ t = d/t  ->  t^2 = d  ->  t = sqrtd  This is NOT a loop you iterate over. This IS the loo",
        "k8": "SRL Locality Validation - The Loop IS The Structure  CRITICAL INSIGHT FOR AGENTS"
      },
      "api_refs": []
    },
    "A1B08B69": {
      "file_path": "examples\\first_run.py",
      "content_hash": 11193134732106484655,
      "topics": [
        "examples",
        "first",
        "run",
        "cubesquare",
        "verify",
        "your",
        "installation",
        "main"
      ],
      "basin": 27,
      "layer": 2,
      "summaries": {
        "k0": "Cubesquare First Run - Verify Your Installation  Run:  python examples/first_run.py  Expected output: All checks should show [OK]",
        "k4": "Cubesquare First Run - Verify Your Installation  Run:  python examples/first_run.py  Expected output: All checks should show [OK]",
        "k8": "Cubesquare First Run - Verify Your Installation  Run:  python examples/first_run"
      },
      "api_refs": []
    },
    "F5E08AFB": {
      "file_path": "examples\\swarm_demo.py",
      "content_hash": 6259811811539088190,
      "topics": [
        "examples",
        "swarm",
        "demo",
        "basin",
        "population",
        "agent",
        "learning",
        "loop",
        "print_header",
        "print_sub",
        "demo_basin_population",
        "demo_agent_swarm"
      ],
      "basin": 94,
      "layer": 7,
      "summaries": {
        "k0": "Swarm Demo -- Basin Population -> Agent Swarm -> Learning Loop  Demonstrates all three systems working together:     1. BasinPopulator discovers semantic meaning in 131 basins     2. Swarm dispatches tasks to 19 agents via I-Logic routing     3. TrainingLoop learns optimal routing from experience  Run: python examples/swarm_demo.py",
        "k4": "Swarm Demo -- Basin Population -> Agent Swarm -> Learning Loop  Demonstrates all three systems working together:     1. BasinPopulator discovers semantic meaning in 131 basins     2. Swarm dispatches ",
        "k8": "Swarm Demo -- Basin Population -> Agent Swarm -> Learning Loop  Demonstrates all"
      },
      "api_refs": []
    },
    "D441082A": {
      "file_path": "examples\\tutorial.py",
      "content_hash": 18302114653251637014,
      "topics": [
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