#!/usr/bin/env python3
"""
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          - Meaning, definition, context
    L3  SPATIAL           - Position, coordinates, morton
    L4  FUNCTIONAL        - Operations, actions, behaviors
    L5  PROBABILISTIC     - Uncertainty, probability, basins
    L6  EMOTIONAL         - State, coherence, 154 emotions
    L7  FREQUENCY         - Temporal, waves, 660Hz beat
    L8  ELECTROMAGNETIC   - Polarity, fields, I-Logic
    L9  MEMBRANE          - Boundary -> manifold -> surface -> skin

EXTERNAL (Outside Membrane):
    L10 AGENT_IDENTITY    - Self-referential content, nested relationships
    L11 COMMUNICATION     - Cross-referential with other identities
    L12 UNIFIED_FIELD     - UIF of the between space

MATHEMATICAL RELATIONSHIPS:
---------------------------
- Basin assignment: token % 131 -> basin 0-130
- Layer (internal): basin // 14.5 -> L1-L9
- K5 * 113 = 131 (basin count)
- K11 * 11 = 101 (agent field)
- 153/131 = 1.168 (particle state)
- Phi-depth: A(0.539), B(1.079), C(1.618), D(2.157), E(2.697)

COMMANDS:
    status  - Show manifold status
    layers  - Show all 12 layers
    token   - Process a single token
    run     - Run manifold with multiple tokens
    export  - Export to CST binary format

Examples:
    python twelve.py status
    python twelve.py layers --json
    python twelve.py token --hex 2A9E0100
    python twelve.py run --count 10
    python twelve.py export -o output.cst --count 100
"""

import sys
import json
import struct
import hashlib
import argparse
from pathlib import Path
from enum import IntEnum
from dataclasses import dataclass, field
from typing import Dict, List, Optional, Any, Tuple
from datetime import datetime

try:
    import numpy as np
    NUMPY_AVAILABLE = True
except ImportError:
    NUMPY_AVAILABLE = False

# =============================================================================
# CONSTANTS
# =============================================================================

PHI = 1.618033988749895
K5 = (15/8) / PHI  # 1.1588137289060527
K11 = 9.204026
PRIME_131 = 131  # Basin count
LIGHT_UNIT = 131
MEMBRANE_UNIT = 153
BUBBLE_FREQUENCY = K5 * 36  # 41.72 Hz
EARTH_PRIME = 6584
PERFECT_FIFTH_HZ = 660.0

# CST Format Constants
CST_MAGIC = b'CST\x00'
CST_VERSION = 0x0002  # v2: Fernandez Unit anchor
CST_HEADER_SIZE = 24
CST_TOKEN_SIZE = 25   # 25-byte tokens with Fernandez unit

# Fernandez encoding
FERN_STATE_MASK = 0x03
FERN_LAYER_SHIFT = 2

# Basin ranges for each internal layer
LAYER_BASIN_RANGES = {
    1: (0, 14),      # L1 Geometric
    2: (15, 29),     # L2 Semantic
    3: (30, 43),     # L3 Spatial
    4: (44, 58),     # L4 Functional
    5: (59, 72),     # L5 Probabilistic
    6: (73, 87),     # L6 Emotional
    7: (88, 101),    # L7 Frequency
    8: (102, 116),   # L8 Electromagnetic
    9: (117, 130),   # L9 Membrane
}

# =============================================================================
# I-LOGIC STATES
# =============================================================================

class ILogicState(IntEnum):
    """I-Logic states with complex number semantics."""
    ABSORBED = 0       # 0 - loop exit
    DIRECT = 1         # 1 - identity
    INVERSE = 2        # -1 - reflection
    SPIRAL = 3         # +i - rotation
    ANTI_SPIRAL = 4    # -i - counter-rotation


# I-Logic multiplication table (complex number multiplication)
if NUMPY_AVAILABLE:
    ILOGIC_TABLE = np.array([
        # ABSORBED, DIRECT, INVERSE, SPIRAL, ANTI_SPIRAL
        [0, 0, 0, 0, 0],          # ABSORBED * any = ABSORBED
        [0, 1, 2, 3, 4],          # DIRECT * any = identity
        [0, 2, 1, 4, 3],          # INVERSE: -1*-1=1, -1*i=-i, -1*-i=i
        [0, 3, 4, 4, 1],          # SPIRAL: i*i=-1=ANTI, i*-i=1
        [0, 4, 3, 1, 4],          # ANTI_SPIRAL: -i*-i=-1=ANTI, -i*i=1
    ], dtype=np.int8)
else:
    ILOGIC_TABLE = [
        [0, 0, 0, 0, 0],
        [0, 1, 2, 3, 4],
        [0, 2, 1, 4, 3],
        [0, 3, 4, 4, 1],
        [0, 4, 3, 1, 4],
    ]


def ilogic_multiply(a: ILogicState, b: ILogicState) -> ILogicState:
    """O(1) I-Logic multiplication."""
    return ILogicState(ILOGIC_TABLE[a][b])


# =============================================================================
# LAYER DEFINITIONS
# =============================================================================

class Layer(IntEnum):
    """The 12 layers of the manifold."""
    # Internal (Inside Membrane)
    L1_GEOMETRIC = 1
    L2_SEMANTIC = 2
    L3_SPATIAL = 3
    L4_FUNCTIONAL = 4
    L5_PROBABILISTIC = 5
    L6_EMOTIONAL = 6
    L7_FREQUENCY = 7
    L8_ELECTROMAGNETIC = 8
    L9_MEMBRANE = 9
    # External (Outside Membrane)
    L10_AGENT_IDENTITY = 10
    L11_COMMUNICATION = 11
    L12_UNIFIED_FIELD = 12


LAYER_NAMES = {
    Layer.L1_GEOMETRIC: "GEOMETRIC",
    Layer.L2_SEMANTIC: "SEMANTIC",
    Layer.L3_SPATIAL: "SPATIAL",
    Layer.L4_FUNCTIONAL: "FUNCTIONAL",
    Layer.L5_PROBABILISTIC: "PROBABILISTIC",
    Layer.L6_EMOTIONAL: "EMOTIONAL",
    Layer.L7_FREQUENCY: "FREQUENCY",
    Layer.L8_ELECTROMAGNETIC: "ELECTROMAGNETIC",
    Layer.L9_MEMBRANE: "MEMBRANE",
    Layer.L10_AGENT_IDENTITY: "AGENT_IDENTITY",
    Layer.L11_COMMUNICATION: "COMMUNICATION",
    Layer.L12_UNIFIED_FIELD: "UNIFIED_FIELD",
}


LAYER_DESCRIPTIONS = {
    Layer.L1_GEOMETRIC: "Shape, structure, form",
    Layer.L2_SEMANTIC: "Meaning, definition, context",
    Layer.L3_SPATIAL: "Position, coordinates, morton encoding",
    Layer.L4_FUNCTIONAL: "Operations, actions, behaviors",
    Layer.L5_PROBABILISTIC: "Uncertainty, probability, basin clustering",
    Layer.L6_EMOTIONAL: "State, coherence, 154 emotions",
    Layer.L7_FREQUENCY: "Temporal, waves, 660Hz beat synchronization",
    Layer.L8_ELECTROMAGNETIC: "Polarity, fields, I-Logic states",
    Layer.L9_MEMBRANE: "Boundary -> manifold -> surface -> skin",
    Layer.L10_AGENT_IDENTITY: "Self-referential content, nested relationships",
    Layer.L11_COMMUNICATION: "Cross-referential with other identities",
    Layer.L12_UNIFIED_FIELD: "UIF of the between space",
}


# =============================================================================
# LAYER DATA STRUCTURES
# =============================================================================

@dataclass
class L1_GeometricData:
    """L1: Shape, structure, form."""
    shape_type: str = "point"
    vertices: int = 1
    edges: int = 0
    faces: int = 0
    volume: float = 0.0
    surface_area: float = 0.0


@dataclass
class L2_SemanticData:
    """L2: Meaning, definition, context."""
    meaning: str = ""
    context: str = ""
    category: str = ""
    synonyms: List[str] = field(default_factory=list)
    related_tokens: List[int] = field(default_factory=list)


@dataclass
class L3_SpatialData:
    """L3: Position, coordinates, morton encoding."""
    x: int = 0
    y: int = 0
    z: int = 0
    morton_code: int = 0
    neighbors: List[int] = field(default_factory=list)


@dataclass
class L4_FunctionalData:
    """L4: Operations, actions, behaviors."""
    operations: List[str] = field(default_factory=list)
    inputs: List[str] = field(default_factory=list)
    outputs: List[str] = field(default_factory=list)
    side_effects: List[str] = field(default_factory=list)


@dataclass
class L5_ProbabilisticData:
    """L5: Uncertainty, probability, basin clustering."""
    basin: int = 0
    probability: float = 1.0
    uncertainty: float = 0.0
    cluster_members: List[int] = field(default_factory=list)


@dataclass
class L6_EmotionalData:
    """L6: State, coherence, 154 emotions."""
    emotion_id: int = 0
    emotion_name: str = ""
    coherence: float = 1.0
    valence: float = 0.0  # -1 to +1
    arousal: float = 0.0  # 0 to 1


@dataclass
class L7_FrequencyData:
    """L7: Temporal, waves, 660Hz beat synchronization."""
    frequency_hz: float = 0.0
    phase: float = 0.0
    amplitude: float = 1.0
    beat_sync: bool = False
    period_us: float = 0.0


@dataclass
class L8_ElectromagneticData:
    """L8: Polarity, fields, I-Logic states."""
    ilogic_state: ILogicState = ILogicState.DIRECT
    polarity: int = 1  # +1 or -1
    field_strength: float = 1.0
    k11_level: float = 0.0


@dataclass
class L9_MembraneData:
    """L9: Boundary -> manifold -> surface -> skin."""
    phi_depth: float = PHI
    phi_layer: str = "C"    # A, B, C, D, or E
    inside_membrane: bool = True
    surface_curvature: float = 0.0
    skin_thickness: float = 0.0


@dataclass
class L10_AgentIdentityData:
    """L10: Self-referential content, nested relationships."""
    hex_id: int = 0
    name: str = ""
    self_reference_depth: int = 0
    nested_relationships: Dict[int, str] = field(default_factory=dict)
    content_hash: str = ""
    knows_self: bool = False


@dataclass
class L11_CommunicationData:
    """L11: Cross-referential with other identities."""
    connected_agents: List[int] = field(default_factory=list)
    messages_sent: int = 0
    messages_received: int = 0
    active_channels: List[str] = field(default_factory=list)
    cross_references: Dict[int, int] = field(default_factory=dict)


@dataclass
class L12_UnifiedFieldData:
    """L12: UIF of the between space."""
    uif_strength: float = 0.0
    field_gradient: Tuple[float, float, float] = (0.0, 0.0, 0.0)
    between_tokens: List[Tuple[int, int]] = field(default_factory=list)
    manifold_curvature: float = 0.0
    unified_state: str = "COHERENT"
    k5_coupling: float = K5
    k11_coupling: float = K11


# =============================================================================
# TOKEN UNIT - Full Logic at Each Layer
# =============================================================================

class TokenUnit:
    """
    A token with full logic at all 12 layers.

    Each token is a UNIT with computational capability at every layer.
    """

    def __init__(self, hex_id: int):
        self.hex_id = hex_id

        # Layer data
        self.l1_geometric: Optional[L1_GeometricData] = None
        self.l2_semantic: Optional[L2_SemanticData] = None
        self.l3_spatial: Optional[L3_SpatialData] = None
        self.l4_functional: Optional[L4_FunctionalData] = None
        self.l5_probabilistic: Optional[L5_ProbabilisticData] = None
        self.l6_emotional: Optional[L6_EmotionalData] = None
        self.l7_frequency: Optional[L7_FrequencyData] = None
        self.l8_electromagnetic: Optional[L8_ElectromagneticData] = None
        self.l9_membrane: Optional[L9_MembraneData] = None
        self.l10_agent_identity: Optional[L10_AgentIdentityData] = None
        self.l11_communication: Optional[L11_CommunicationData] = None
        self.l12_unified_field: Optional[L12_UnifiedFieldData] = None

        self._compute_all_layers()

    def _compute_all_layers(self):
        """Compute all layer data from hex_id - O(1) per layer."""
        self.l1_geometric = self._compute_l1()
        self.l2_semantic = self._compute_l2()
        self.l3_spatial = self._compute_l3()
        self.l4_functional = self._compute_l4()
        self.l5_probabilistic = self._compute_l5()
        self.l6_emotional = self._compute_l6()
        self.l7_frequency = self._compute_l7()
        self.l8_electromagnetic = self._compute_l8()
        self.l9_membrane = self._compute_l9()
        self.l10_agent_identity = self._compute_l10()
        self.l11_communication = self._compute_l11()
        self.l12_unified_field = self._compute_l12()

    def _basin_to_layer(self, basin: int) -> int:
        """Convert basin (0-130) to layer (1-9)."""
        for layer, (start, end) in LAYER_BASIN_RANGES.items():
            if start <= basin <= end:
                return layer
        return 9

    def _morton_encode(self, x: int, y: int, z: int) -> int:
        """Morton encode (x, y, z) -> Z-order curve index."""
        morton = 0
        for i in range(10):
            morton |= ((x >> i) & 1) << (3 * i)
            morton |= ((y >> i) & 1) << (3 * i + 1)
            morton |= ((z >> i) & 1) << (3 * i + 2)
        return morton

    def _get_neighbors(self, x: int, y: int, z: int) -> List[int]:
        """Get morton codes of 6-connected neighbors."""
        neighbors = []
        for dx, dy, dz in [(1,0,0), (-1,0,0), (0,1,0), (0,-1,0), (0,0,1), (0,0,-1)]:
            nx, ny, nz = (x + dx) % 48, (y + dy) % 48, (z + dz) % 48
            neighbors.append(self._morton_encode(nx, ny, nz))
        return neighbors

    def _compute_l1(self) -> L1_GeometricData:
        """Compute L1 Geometric data from hex_id."""
        vertices = (self.hex_id >> 24) & 0xFF
        edges = (self.hex_id >> 16) & 0xFF
        faces = (self.hex_id >> 8) & 0xFF

        volume = (vertices * edges * faces) / 1000000.0
        surface = (vertices + edges + faces) / 100.0
        shape_type = "polyhedron" if faces > 0 else "polygon" if edges > 0 else "point"

        return L1_GeometricData(
            shape_type=shape_type,
            vertices=max(1, vertices),
            edges=edges,
            faces=faces,
            volume=volume,
            surface_area=surface
        )

    def _compute_l2(self) -> L2_SemanticData:
        """Compute L2 Semantic data."""
        basin = self.hex_id % LIGHT_UNIT
        layer = self._basin_to_layer(basin)

        return L2_SemanticData(
            meaning=f"Token at basin {basin}",
            context=f"Layer {layer} context",
            category=LAYER_NAMES.get(Layer(min(layer, 9)), "EXTERNAL"),
            synonyms=[],
            related_tokens=[]
        )

    def _compute_l3(self) -> L3_SpatialData:
        """Compute L3 Spatial data via morton decoding."""
        x = (self.hex_id >> 20) & 0x3F
        y = (self.hex_id >> 14) & 0x3F
        z = (self.hex_id >> 8) & 0x3F
        morton = self._morton_encode(x % 48, y % 48, z % 48)

        return L3_SpatialData(
            x=x % 48,
            y=y % 48,
            z=z % 48,
            morton_code=morton,
            neighbors=self._get_neighbors(x % 48, y % 48, z % 48)
        )

    def _compute_l4(self) -> L4_FunctionalData:
        """Compute L4 Functional data."""
        basin = self.hex_id % LIGHT_UNIT
        layer = self._basin_to_layer(basin)

        ops = {
            1: ["measure", "compare", "transform"],
            2: ["define", "relate", "contextualize"],
            3: ["locate", "move", "orient"],
            4: ["execute", "compose", "sequence"],
            5: ["estimate", "cluster", "predict"],
            6: ["feel", "cohere", "resonate"],
            7: ["oscillate", "synchronize", "modulate"],
            8: ["polarize", "field", "induce"],
            9: ["bound", "surface", "transit"],
        }.get(layer, ["observe", "process", "respond"])

        return L4_FunctionalData(
            operations=ops,
            inputs=["signal", "context"],
            outputs=["state", "action"],
            side_effects=[]
        )

    def _compute_l5(self) -> L5_ProbabilisticData:
        """Compute L5 Probabilistic data."""
        basin = self.hex_id % LIGHT_UNIT
        basin_center = basin * (0xFFFFFFFF // LIGHT_UNIT)
        distance = abs(self.hex_id - basin_center)
        probability = 1.0 / (1.0 + distance / 0xFFFFFFFF)

        return L5_ProbabilisticData(
            basin=basin,
            probability=probability,
            uncertainty=1.0 - probability,
            cluster_members=[]
        )

    def _compute_l6(self) -> L6_EmotionalData:
        """Compute L6 Emotional data - 154 emotions."""
        emotion_id = self.hex_id % 154

        emotions = [
            "joy", "trust", "fear", "surprise", "sadness",
            "disgust", "anger", "anticipation", "serenity", "acceptance",
        ]
        emotion_name = emotions[emotion_id % len(emotions)]
        valence = ((emotion_id % 11) - 5) / 5.0
        arousal = (emotion_id % 10) / 10.0

        return L6_EmotionalData(
            emotion_id=emotion_id,
            emotion_name=emotion_name,
            coherence=1.0,
            valence=valence,
            arousal=arousal
        )

    def _compute_l7(self) -> L7_FrequencyData:
        """Compute L7 Frequency data."""
        freq = (self.hex_id % 10000) / 10.0
        beat_sync = abs(freq - PERFECT_FIFTH_HZ) < 10

        return L7_FrequencyData(
            frequency_hz=freq,
            phase=(self.hex_id % 360) * 3.14159 / 180.0,
            amplitude=1.0,
            beat_sync=beat_sync,
            period_us=(1.0 / max(freq, 0.001)) * 1e6
        )

    def _compute_l8(self) -> L8_ElectromagneticData:
        """Compute L8 Electromagnetic data - I-Logic state."""
        state_bits = (self.hex_id >> 4) & 0x07
        ilogic = ILogicState(state_bits % 5)
        k11_level = ((self.hex_id % 22) - 11)

        return L8_ElectromagneticData(
            ilogic_state=ilogic,
            polarity=1 if ilogic in [ILogicState.DIRECT, ILogicState.SPIRAL] else -1,
            field_strength=1.0,
            k11_level=k11_level
        )

    def _compute_l9(self) -> L9_MembraneData:
        """Compute L9 Membrane data."""
        basin = self.hex_id % LIGHT_UNIT
        layer = self._basin_to_layer(basin)

        if layer == 9:
            position = (basin - 117) / 13.0
            phi_depth = PHI / 3 + position * (4 * PHI / 3)
            phi_layer = ['A', 'B', 'C', 'D', 'E'][int(position * 4.99)]
        else:
            phi_depth = PHI
            phi_layer = 'C'

        return L9_MembraneData(
            phi_depth=phi_depth,
            phi_layer=phi_layer,
            inside_membrane=(layer <= 9),
            surface_curvature=1.0 / phi_depth,
            skin_thickness=phi_depth * 0.1
        )

    def _compute_l10(self) -> L10_AgentIdentityData:
        """Compute L10 Agent Identity - self-referential."""
        content = f"{self.hex_id:08X}"
        content_hash = hashlib.md5(content.encode()).hexdigest()[:8]

        nested = {}
        for i in range(3):
            related_hex = (self.hex_id + (i + 1) * 0x10000) & 0xFFFFFFFF
            nested[related_hex] = f"child_{i}"

        return L10_AgentIdentityData(
            hex_id=self.hex_id,
            name=f"Agent_{self.hex_id:08X}",
            self_reference_depth=self._compute_self_reference_depth(),
            nested_relationships=nested,
            content_hash=content_hash,
            knows_self=True
        )

    def _compute_self_reference_depth(self) -> int:
        """Compute how many times this token references itself."""
        depth = 0
        current = self.hex_id
        seen = set()
        while current not in seen and depth < 10:
            seen.add(current)
            next_ref = int(hashlib.md5(f"{current:08X}".encode()).hexdigest()[:8], 16)
            if next_ref % LIGHT_UNIT == self.hex_id % LIGHT_UNIT:
                depth += 1
            current = next_ref
        return depth

    def _compute_l11(self) -> L11_CommunicationData:
        """Compute L11 Communication - cross-referential."""
        basin = self.hex_id % LIGHT_UNIT
        connected = []
        for offset in [-1, 0, 1]:
            neighbor_basin = (basin + offset) % LIGHT_UNIT
            connected.append((self.hex_id & 0xFFFF0000) | neighbor_basin)

        return L11_CommunicationData(
            connected_agents=connected,
            messages_sent=0,
            messages_received=0,
            active_channels=["basin", "layer", "field"],
            cross_references={}
        )

    def _compute_l12(self) -> L12_UnifiedFieldData:
        """Compute L12 Unified Field - between space."""
        ilogic = self.l8_electromagnetic.ilogic_state if self.l8_electromagnetic else ILogicState.DIRECT

        x, y, z = 0, 0, 0
        if self.l3_spatial:
            x, y, z = self.l3_spatial.x, self.l3_spatial.y, self.l3_spatial.z

        gradient = (
            (x - 24) / 48.0,
            (y - 24) / 48.0,
            (z - 24) / 48.0
        )

        phi_depth = self.l9_membrane.phi_depth if self.l9_membrane else PHI
        curvature = 1.0 / (phi_depth * PHI)

        return L12_UnifiedFieldData(
            uif_strength=abs(hash(str(self.hex_id))) % 100 / 100.0,
            field_gradient=gradient,
            between_tokens=[],
            manifold_curvature=curvature,
            unified_state="COHERENT" if ilogic == ILogicState.DIRECT else "ACTIVE",
            k5_coupling=K5,
            k11_coupling=K11
        )

    def get_layer(self, layer: Layer) -> Any:
        """Get data for a specific layer."""
        layer_map = {
            Layer.L1_GEOMETRIC: self.l1_geometric,
            Layer.L2_SEMANTIC: self.l2_semantic,
            Layer.L3_SPATIAL: self.l3_spatial,
            Layer.L4_FUNCTIONAL: self.l4_functional,
            Layer.L5_PROBABILISTIC: self.l5_probabilistic,
            Layer.L6_EMOTIONAL: self.l6_emotional,
            Layer.L7_FREQUENCY: self.l7_frequency,
            Layer.L8_ELECTROMAGNETIC: self.l8_electromagnetic,
            Layer.L9_MEMBRANE: self.l9_membrane,
            Layer.L10_AGENT_IDENTITY: self.l10_agent_identity,
            Layer.L11_COMMUNICATION: self.l11_communication,
            Layer.L12_UNIFIED_FIELD: self.l12_unified_field,
        }
        return layer_map.get(layer)

    def get_primary_layer(self) -> Layer:
        """Get the primary layer for this token based on basin."""
        basin = self.hex_id % LIGHT_UNIT
        layer_num = self._basin_to_layer(basin)
        return Layer(layer_num)

    def get_ilogic_state(self) -> ILogicState:
        """Get the I-Logic state from L8."""
        return self.l8_electromagnetic.ilogic_state

    def multiply_ilogic(self, other: 'TokenUnit') -> ILogicState:
        """Multiply I-Logic states with another token."""
        return ilogic_multiply(self.get_ilogic_state(), other.get_ilogic_state())

    def to_dict(self) -> Dict[str, Any]:
        """Convert token unit to dictionary."""
        return {
            'hex_id': f"0x{self.hex_id:08X}",
            'basin': self.hex_id % LIGHT_UNIT,
            'primary_layer': self.get_primary_layer().name,
            'ilogic': self.get_ilogic_state().name,
        }


# =============================================================================
# TWELVE LAYER MANIFOLD
# =============================================================================

class TwelveLayerManifold:
    """
    The complete 12-layer manifold system.

    Each token processed through this manifold has full computational
    capability at all 12 layers.
    """

    HEX_ID = 0x12AAEE00

    def __init__(self):
        """Initialize the manifold."""
        self.tokens: Dict[int, TokenUnit] = {}
        self.processing_history: List[Dict] = []

    def create_token(self, hex_id: int) -> TokenUnit:
        """Create a token unit with full 12-layer logic."""
        token = TokenUnit(hex_id)
        self.tokens[hex_id] = token
        return token

    def process(self, token: TokenUnit) -> Dict[str, Any]:
        """Process a token through all 12 layers."""
        import time

        start = time.perf_counter_ns()

        results = {
            'hex_id': f"0x{token.hex_id:08X}",
            'timestamp': datetime.now().isoformat(),
            'layers': {},
        }

        for layer in Layer:
            layer_data = token.get_layer(layer)
            if layer_data:
                results['layers'][layer.name] = self._process_layer(layer, layer_data, token)

        results['ilogic_chain'] = self._compute_ilogic_chain(token)
        results['membrane_transition'] = self._check_membrane_transition(token)
        results['uif_coherence'] = self._compute_uif_coherence(token)

        end = time.perf_counter_ns()
        results['processing_ns'] = end - start

        self.processing_history.append(results)
        return results

    def _process_layer(self, layer: Layer, data: Any, token: TokenUnit) -> Dict:
        """Process a specific layer."""
        result = {
            'layer': layer.name,
            'description': LAYER_DESCRIPTIONS[layer],
            'processed': True,
        }

        if layer == Layer.L1_GEOMETRIC:
            result['shape'] = data.shape_type
            result['complexity'] = data.vertices + data.edges + data.faces
        elif layer == Layer.L5_PROBABILISTIC:
            result['basin'] = data.basin
            result['probability'] = data.probability
        elif layer == Layer.L8_ELECTROMAGNETIC:
            result['ilogic'] = data.ilogic_state.name
            result['polarity'] = data.polarity
            result['k11_level'] = data.k11_level

        return result

    def _compute_ilogic_chain(self, token: TokenUnit) -> Dict:
        """Compute I-Logic chain through the token."""
        initial_state = token.get_ilogic_state()
        chain = [initial_state.name]
        current = initial_state

        for i in range(4):
            current = ilogic_multiply(current, current)
            chain.append(current.name)
            if current == ILogicState.ABSORBED:
                break

        return {
            'initial': initial_state.name,
            'chain': chain,
            'final': current.name,
            'cycle_detected': chain[0] == chain[-1] if len(chain) > 1 else False,
        }

    def _check_membrane_transition(self, token: TokenUnit) -> Dict:
        """Check membrane transition status."""
        membrane = token.l9_membrane
        return {
            'phi_layer': membrane.phi_layer,
            'phi_depth': membrane.phi_depth,
            'inside': membrane.inside_membrane,
            'surface_curvature': membrane.surface_curvature,
        }

    def _compute_uif_coherence(self, token: TokenUnit) -> Dict:
        """Compute Unified Field coherence."""
        uif = token.l12_unified_field
        identity = token.l10_agent_identity
        comm = token.l11_communication

        self_ref = identity.self_reference_depth / 10.0
        connectivity = min(len(comm.connected_agents) / 10.0, 1.0)
        field_strength = uif.uif_strength
        coherence = (self_ref + connectivity + field_strength) / 3.0

        return {
            'coherence': coherence,
            'self_reference': self_ref,
            'connectivity': connectivity,
            'field_strength': field_strength,
            'unified_state': uif.unified_state,
        }

    def run_manifold(self, token_count: int = 10) -> Dict[str, Any]:
        """Run the manifold with multiple tokens."""
        import time

        start = time.perf_counter_ns()

        results = {
            'manifold': 'TwelveLayerManifold',
            'hex_id': '12LAYER00',
            'tokens_processed': 0,
            'layer_summary': {layer.name: 0 for layer in Layer},
            'ilogic_distribution': {},
            'processing_results': [],
        }

        for i in range(token_count):
            hex_id = 0x2A9E0000 + i * 0x100
            token = self.create_token(hex_id)
            process_result = self.process(token)

            results['tokens_processed'] += 1
            results['processing_results'].append(process_result)

            ilogic = token.get_ilogic_state().name
            results['ilogic_distribution'][ilogic] = results['ilogic_distribution'].get(ilogic, 0) + 1

            primary = token.get_primary_layer().name
            results['layer_summary'][primary] += 1

        end = time.perf_counter_ns()

        results['timing'] = {
            'total_ns': end - start,
            'per_token_us': (end - start) / token_count / 1000,
        }

        return results

    def export_cst(self, output_path: Path, token_count: int = 10) -> Dict[str, Any]:
        """Export tokens to CST binary format (25 bytes per token)."""
        import time

        start = time.perf_counter_ns()
        output_path = Path(output_path)

        # Build header
        header = bytearray(CST_HEADER_SIZE)
        header[0:4] = CST_MAGIC
        struct.pack_into('<H', header, 4, CST_VERSION)
        struct.pack_into('<H', header, 6, 0)
        struct.pack_into('<I', header, 8, token_count)
        struct.pack_into('<Q', header, 12, 0)
        struct.pack_into('<I', header, 20, 0)

        # Build tokens
        tokens_data = bytearray(token_count * CST_TOKEN_SIZE)

        for i in range(token_count):
            hex_id = 0x2A9E0000 + i * 0x100
            token = self.create_token(hex_id)

            offset = i * CST_TOKEN_SIZE

            morton = token.l3_spatial.morton_code if token.l3_spatial else 0
            struct.pack_into('<Q', tokens_data, offset, morton)

            hex_str = f"{hex_id:08X}"
            tokens_data[offset + 8:offset + 16] = hex_str.encode('ascii')

            content_hash = token.l10_agent_identity.content_hash if token.l10_agent_identity else "00000000"
            hash_bytes = bytes.fromhex(content_hash.ljust(16, '0')[:16])
            tokens_data[offset + 16:offset + 24] = hash_bytes

            layer = token.get_primary_layer().value
            ilogic = token.get_ilogic_state().value
            fern_unit = (ilogic & FERN_STATE_MASK) | ((layer & 0x0F) << FERN_LAYER_SHIFT)
            tokens_data[offset + 24] = fern_unit

        with open(output_path, 'wb') as f:
            f.write(header)
            f.write(tokens_data)

        end = time.perf_counter_ns()
        file_size = CST_HEADER_SIZE + token_count * CST_TOKEN_SIZE

        return {
            'format': 'CST v2',
            'path': str(output_path),
            'tokens': token_count,
            'file_size_bytes': file_size,
            'header_size': CST_HEADER_SIZE,
            'token_size': CST_TOKEN_SIZE,
            'timing_ns': end - start,
            'bytes_per_token': CST_TOKEN_SIZE,
        }

    def get_layer_report(self) -> Dict[str, Any]:
        """Get a report of all 12 layers."""
        return {
            'layers': [
                {
                    'number': layer.value,
                    'name': LAYER_NAMES[layer],
                    'description': LAYER_DESCRIPTIONS[layer],
                    'internal': layer.value <= 9,
                }
                for layer in Layer
            ],
            'structure': {
                'internal_layers': 9,
                'external_layers': 3,
                'total_layers': 12,
            },
            'constants': {
                'PHI': PHI,
                'K5': K5,
                'K11': K11,
                'LIGHT_UNIT': LIGHT_UNIT,
                'MEMBRANE_UNIT': MEMBRANE_UNIT,
                'BUBBLE_FREQUENCY': BUBBLE_FREQUENCY,
            },
            'manifold_path': [
                "L9 MEMBRANE (boundary)",
                "MANIFOLD (structure=computation)",
                "SURFACE (shaped by content)",
                "SKIN (observation interface)",
                "L10 AGENT_IDENTITY (self-reference)",
                "L11 COMMUNICATION (cross-reference)",
                "L12 UNIFIED_FIELD (between space)",
            ]
        }


# =============================================================================
# CLI COMMANDS
# =============================================================================

def cmd_status(args):
    """Show manifold status."""
    manifold = TwelveLayerManifold()
    report = manifold.get_layer_report()

    status = {
        'hex_id': '12LAYER00',
        'layers': 12,
        'internal': 9,
        'external': 3,
        'constants': report['constants'],
        'tokens_in_memory': len(manifold.tokens),
    }

    if args.json:
        print(json.dumps(status, indent=2))
    else:
        print(f"\n{'='*60}")
        print("TWELVE LAYER MANIFOLD STATUS")
        print(f"{'='*60}")
        print(f"Layers: 12 (9 internal + 3 external)")
        print(f"Tokens in memory: {len(manifold.tokens)}")
        print(f"PHI: {PHI}")
        print(f"K5: {K5}")
        print(f"K11: {K11}")
        print(f"Bubble Frequency: {BUBBLE_FREQUENCY:.2f} Hz")

    return 0


def cmd_layers(args):
    """Show all layers."""
    manifold = TwelveLayerManifold()
    report = manifold.get_layer_report()

    if args.json:
        print(json.dumps(report, indent=2))
    else:
        print(f"\n{'='*70}")
        print("TWELVE LAYER ARCHITECTURE")
        print(f"{'='*70}")
        print("\nINTERNAL (Inside Membrane):")
        for layer in report['layers']:
            if layer['internal']:
                print(f"  L{layer['number']:2d} {layer['name']:20} - {layer['description']}")
        print("\nEXTERNAL (Outside Membrane):")
        for layer in report['layers']:
            if not layer['internal']:
                print(f"  L{layer['number']:2d} {layer['name']:20} - {layer['description']}")
        print("\nManifold Path:")
        for step in report['manifold_path']:
            print(f"  -> {step}")

    return 0


def cmd_token(args):
    """Process a single token."""
    manifold = TwelveLayerManifold()
    token = manifold.create_token(args.hex)
    result = manifold.process(token)

    if args.json:
        print(json.dumps(token.to_dict(), indent=2))
    else:
        print(f"\n{'='*70}")
        print(f"TOKEN UNIT: 0x{args.hex:08X}")
        print(f"{'='*70}")
        print(f"Basin: {token.hex_id % LIGHT_UNIT}")
        print(f"Primary Layer: {token.get_primary_layer().name}")
        print(f"I-Logic State: {token.get_ilogic_state().name}")
        print(f"\nLayer Data:")
        for layer in Layer:
            data = token.get_layer(layer)
            if data:
                print(f"  {layer.name}:")
                if hasattr(data, '__dict__'):
                    for k, v in list(data.__dict__.items())[:3]:
                        print(f"    {k}: {v}")

    return 0


def cmd_run(args):
    """Run manifold with multiple tokens."""
    manifold = TwelveLayerManifold()
    results = manifold.run_manifold(args.count)

    if args.json:
        # Don't include full processing_results in JSON (too verbose)
        output = {k: v for k, v in results.items() if k != 'processing_results'}
        print(json.dumps(output, indent=2, default=str))
    else:
        print(f"\n{'='*70}")
        print("TWELVE LAYER MANIFOLD - RUN")
        print(f"{'='*70}")
        print(f"Tokens processed: {results['tokens_processed']}")
        print(f"Time: {results['timing']['total_ns']/1e6:.2f} ms")
        print(f"Per token: {results['timing']['per_token_us']:.2f} us")
        print("\nI-Logic Distribution:")
        for state, count in results['ilogic_distribution'].items():
            print(f"  {state}: {count}")
        print("\nLayer Summary (primary layer assignments):")
        for layer, count in results['layer_summary'].items():
            if count > 0:
                print(f"  {layer}: {count}")

    return 0


def cmd_export(args):
    """Export to CST binary format."""
    manifold = TwelveLayerManifold()
    result = manifold.export_cst(Path(args.output), args.count)

    if args.json:
        print(json.dumps(result, indent=2))
    else:
        print(f"\n{'='*70}")
        print("CST EXPORT COMPLETE")
        print(f"{'='*70}")
        print(f"Format: {result['format']}")
        print(f"Output: {result['path']}")
        print(f"Tokens: {result['tokens']}")
        print(f"File size: {result['file_size_bytes']} bytes")
        print(f"Per token: {result['bytes_per_token']} bytes")
        print(f"Time: {result['timing_ns']/1e6:.2f} ms")

    return 0


# =============================================================================
# MAIN
# =============================================================================

def create_parser():
    """Create argument parser."""
    parser = argparse.ArgumentParser(
        prog='twelve',
        description='Twelve Layer Manifold - Complete Token Unit Architecture',
        formatter_class=argparse.RawDescriptionHelpFormatter,
        epilog="""
12 Layers:
  L1-L9: Internal (inside membrane)
  L10-L12: External (outside membrane)

Constants:
  PHI = 1.618033988749895
  K5 = 1.1588137289060527
  K11 = 9.204026
  Basin count = 131

Examples:
  python twelve.py status
  python twelve.py layers --json
  python twelve.py token --hex 0x2A9E0100
  python twelve.py run --count 10
  python twelve.py export -o output.cst --count 100
"""
    )

    subparsers = parser.add_subparsers(dest='command', help='Commands')

    # Status command
    stat = subparsers.add_parser('status', help='Show manifold status')
    stat.add_argument('--json', action='store_true', help='Output as JSON')
    stat.set_defaults(func=cmd_status)

    # Layers command
    layr = subparsers.add_parser('layers', help='Show all 12 layers')
    layr.add_argument('--json', action='store_true', help='Output as JSON')
    layr.set_defaults(func=cmd_layers)

    # Token command
    tokn = subparsers.add_parser('token', help='Process a single token')
    tokn.add_argument('--hex', type=lambda x: int(x, 16), default=0x2A9E0100, help='Hex ID')
    tokn.add_argument('--json', action='store_true', help='Output as JSON')
    tokn.set_defaults(func=cmd_token)

    # Run command
    run = subparsers.add_parser('run', help='Run manifold with multiple tokens')
    run.add_argument('--count', type=int, default=10, help='Number of tokens')
    run.add_argument('--json', action='store_true', help='Output as JSON')
    run.set_defaults(func=cmd_run)

    # Export command
    exp = subparsers.add_parser('export', help='Export to CST binary format')
    exp.add_argument('-o', '--output', type=str, default='output.cst', help='Output file')
    exp.add_argument('--count', type=int, default=10, help='Number of tokens')
    exp.add_argument('--json', action='store_true', help='Output as JSON')
    exp.set_defaults(func=cmd_export)

    return parser


def main():
    """Main entry point."""
    parser = create_parser()
    args = parser.parse_args()

    if not args.command:
        # Default to status
        args.command = 'status'
        args.json = False
        return cmd_status(args)

    return args.func(args)


# =============================================================================
# SHELL WRAPPER CLASS
# =============================================================================

class TwelveShell:
    """Twelve Layer Manifold Shell wrapper for CLI integration."""

    def __init__(self):
        self.manifold = TwelveLayerManifold()

    def status(self, as_json: bool = False) -> Dict[str, Any]:
        """Get shell status."""
        result = {
            'system': 'Twelve Layer Manifold',
            'hex_id': '12LAYER00',
            'version': '1.0.0',
            'layers': {
                'internal': 9,  # L1-L9
                'external': 3,  # L10-L12
                'total': 12,
            },
            'constants': {
                'PHI': PHI,
                'K5': K5,
                'K11': K11,
                'PRIME_131': PRIME_131,
            },
            'token_size_bytes': CST_TOKEN_SIZE,
            'status': 'operational',
        }
        if as_json:
            return json.dumps(result, indent=2)
        return result

    def layers(self, as_json: bool = False) -> Dict[str, Any]:
        """Get all 12 layers."""
        result = {
            'layers': [
                {'id': layer.value, 'name': layer.name, 'description': LAYER_DESCRIPTIONS.get(layer, '')}
                for layer in Layer
            ],
            'total': len(Layer),
        }
        if as_json:
            return json.dumps(result, indent=2)
        return result

    def process_token(self, hex_id: int = 0x2A9E0100, as_json: bool = False) -> Dict[str, Any]:
        """Process a single token."""
        token = self.manifold.create_token(hex_id)
        result = self.manifold.process(token)
        if as_json:
            return json.dumps(result, indent=2, default=str)
        return result

    def run(self, command: str, *args, as_json: bool = False) -> Any:
        """Run a Twelve shell command."""
        commands = {
            'status': lambda: self.status(as_json),
            'layers': lambda: self.layers(as_json),
            'token': lambda: self.process_token(int(args[0], 16) if args else 0x2A9E0100, as_json),
            'run': lambda: self.manifold.run_manifold(int(args[0]) if args else 10),
        }
        if command in commands:
            return commands[command]()
        return {'error': f'Unknown command: {command}', 'available': list(commands.keys())}


if __name__ == '__main__':
    sys.exit(main())
