Fix #679: Generate GENOME.md for turboquant

- Created comprehensive GENOME.md with full codebase analysis
- Added architecture diagram (Mermaid)
- Documented entry points and data flow
- Identified key abstractions
- Mapped API surface (C, Metal, CLI)
- Identified test coverage gaps
- Documented security considerations
- Added basic test suite (9 tests passing)

Key findings:
- 73.4% KV memory savings (turbo4 vs f16)
- ~1% prompt overhead, ~11% generation overhead
- PolarQuant + QJL = 3.5 bits/channel
- Metal shaders exist on feature branch
- CPU reference incompatible with Metal dequant
- QJL infrastructure present but disabled

Test coverage gaps:
- No unit tests for encode/decode
- No integration tests
- No perplexity runner (corpus exists)
- No Metal vs CPU parity tests

Security considerations:
- Buffer overflow risk in bit packing
- No constant-time implementation
- No safety wrapper for C/C++ code

GENOME.md

@@ -0,0 +1,323 @@
+# GENOME.md — TurboQuant
+
+*Generated: 2026-04-14 | Codebase Genome Analysis*
+
+## Project Overview
+
+**TurboQuant** is a KV cache compression system for local inference on Apple Silicon. It implements Google's TurboQuant algorithm (ICLR 2026) to achieve ~73% memory savings with minimal quality loss.
+
+### Core Value Proposition
+- **Problem**: Large language models (27B+) require massive KV cache memory at long contexts
+- **Solution**: Three-stage compression (PolarQuant + QJL) reduces KV cache to ~3.5 bits/channel
+- **Result**: 128K context on 36GB hardware becomes viable (vs impossible at FP16)
+
+### Key Metrics
+- **Compression**: 73.4% KV memory savings (turbo4 vs f16)
+- **Quality**: ~1% prompt overhead, ~11% generation overhead
+- **Target**: qwen3.5:27b at 128K context within 36GB unified memory
+
+## Architecture
+
+```mermaid
+graph TB
+    subgraph "Input Layer"
+        Q[Query Vector Q]
+        K[Key Vector K]
+        V[Value Vector V]
+    end
+    
+    subgraph "TurboQuant Compression"
+        WHT[Walsh-Hadamard Transform]
+        PQ[PolarQuant Encode]
+        QJL[QJL Residual]
+        PACK[Bit Packing]
+    end
+    
+    subgraph "KV Cache Storage"
+        CACHE[Compressed KV Cache]
+        NORMS[Radius Norms FP16]
+    end
+    
+    subgraph "Decompression & Attention"
+        UNPACK[Bit Unpack]
+        DEQ[PolarQuant Decode]
+        FWHT[Inverse WHT]
+        ATTEN[Attention Compute]
+    end
+    
+    subgraph "Output"
+        SCORES[Attention Scores]
+        OUT[Weighted Values]
+    end
+    
+    K --> WHT
+    WHT --> PQ
+    PQ --> PACK
+    PACK --> CACHE
+    PQ --> NORMS
+    
+    V --> WHT
+    WHT --> PQ
+    PQ --> PACK
+    PACK --> CACHE
+    
+    CACHE --> UNPACK
+    NORMS --> DEQ
+    UNPACK --> DEQ
+    DEQ --> FWHT
+    
+    Q --> ATTEN
+    FWHT --> ATTEN
+    ATTEN --> SCORES
+    SCORES --> OUT
+    
+    style WHT fill:#e1f5fe
+    style PQ fill:#fff3e0
+    style QJL fill:#f3e5f5
+    style ATTEN fill:#e8f5e8
+```
+
+## Entry Points
+
+### Primary Entry: Metal Shaders
+- **File**: `ggml-metal-turbo.metal`
+- **Functions**:
+  - `kernel_fwht_128`: Walsh-Hadamard transform (GPU)
+  - `kernel_turbo4_dequant`: 4-bit dequantization (hot path)
+  - `kernel_attention_turbo4`: Fused attention (conceptual)
+
+### CPU Reference Implementation
+- **File**: `llama-turbo.cpp`
+- **Functions**:
+  - `polar_quant_encode_turbo4`: Encode (CPU reference)
+  - `polar_quant_decode_turbo4`: Decode (CPU reference)
+  - `fwht`: Fast Walsh-Hadamard transform
+
+### Benchmarking
+- **File**: `benchmarks/run_benchmarks.py`
+- **Entry**: CLI tool for measuring TTFT, tokens/sec, memory
+- **Backends**: Ollama, llama-server
+
+### Configuration
+- **File**: `profiles/hermes-profile-gemma4-turboquant.yaml`
+- **Purpose**: Hermes agent profile for TurboQuant deployment
+
+## Data Flow
+
+```
+1. Model Load
+   ├── Load GGUF model weights
+   ├── Initialize Lloyd-Max codebook (16 centroids for turbo4)
+   ├── Initialize WHT rotation matrix (128×128)
+   └── Set per-layer adaptive mode (TURBO_LAYER_ADAPTIVE)
+
+2. Forward Pass (per token)
+   ├── Compute Q, K, V projections
+   ├── Compress K, V via PolarQuant:
+   │   ├── Apply WHT rotation (O(d log d))
+   │   ├── Compute L2 norm (radius)
+   │   ├── Quantize coordinates to 4-bit indices
+   │   └── Pack indices + store radius
+   ├── Store compressed K, V in cache
+   └── Attention:
+       ├── Decompress K from cache (hot path)
+       ├── Compute Q·K^T scores
+       ├── Apply softmax
+       ├── Decompress V from cache
+       └── Compute weighted sum
+
+3. Generation
+   ├── Append new token to sequence
+   ├── Extend KV cache with compressed K, V
+   └── Continue forward pass
+```
+
+## Key Abstractions
+
+### 1. PolarQuant Codec
+- **Purpose**: Compress/decompress KV vectors
+- **Algorithm**: WHT → polar coordinates → Lloyd-Max quantization
+- **Interface**: `polar_quant_encode_turbo4()` / `polar_quant_decode_turbo4()`
+
+### 2. Walsh-Hadamard Transform
+- **Purpose**: Energy-spreading rotation (makes distribution predictable)
+- **Property**: Orthogonal (preserves inner products)
+- **Complexity**: O(d log d) vs O(d²) for dense rotation
+
+### 3. Lloyd-Max Codebook
+- **Purpose**: Optimal scalar quantization for known distribution
+- **Size**: 16 entries for turbo4 (4-bit)
+- **Key**: Precomputed, fixed (no per-vector calibration)
+
+### 4. Per-Layer Adaptive Quantization
+- **Purpose**: Protect sensitive layers (first/last) with higher precision
+- **Modes**: 7 modes (0=uniform, 7=recommended)
+- **Mechanism**: `TURBO_LAYER_ADAPTIVE` environment variable
+
+## API Surface
+
+### C API (llama-turbo.h)
+```c
+// Encode: float → 4-bit packed
+void polar_quant_encode_turbo4(
+    const float* src,    // Input [d]
+    uint8_t* dst,        // Output [d/2] packed 4-bit
+    float* norm,         // Output L2 norm
+    int d                // Dimension (must be power of 2)
+);
+
+// Decode: 4-bit packed → float
+void polar_quant_decode_turbo4(
+    const uint8_t* src,  // Input [d/2] packed 4-bit
+    float* dst,          // Output [d]
+    float norm,          // Input L2 norm
+    int d                // Dimension
+);
+```
+
+### Metal Shaders (GPU)
+```metal
+// Walsh-Hadamard transform (in-place)
+kernel void kernel_fwht_128(
+    device float* data [[buffer(0)]],
+    uint tid [[thread_position_in_grid]]
+);
+
+// 4-bit dequantization (hot path)
+kernel void kernel_turbo4_dequant(
+    device const uchar* src [[buffer(0)]],
+    device const float* norms [[buffer(1)]],
+    device float* dst [[buffer(2)]],
+    uint tid [[thread_position_in_grid]]
+);
+```
+
+### llama-server CLI
+```bash
+llama-server \
+  -m model.gguf \
+  -ctk turbo4 -ctv turbo4 \  # KV cache type
+  -c 131072 \                 # Context length
+  --port 11434                # API port
+```
+
+### Environment Variables
+- `TURBO_LAYER_ADAPTIVE`: Per-layer quantization mode (0-7)
+- `TURBO4_USE_4BIT`: Enable 4-bit mode (default: 1)
+
+## Test Coverage Gaps
+
+### Current State
+- **Unit tests**: ❌ None in this repo
+- **Integration tests**: ❌ None
+- **Benchmark tests**: ✅ `benchmarks/run_benchmarks.py`
+- **Perplexity tests**: ⚠️ Corpus exists (`corpora/wiki.test.raw`) but no runner
+
+### Critical Missing Tests
+1. **Encode/Decode Roundtrip**: Verify `decode(encode(x)) ≈ x`
+2. **Inner Product Preservation**: Verify `Q·K ≈ Q·dequant(quant(K))`
+3. **WHT Orthogonality**: Verify `WHT^T · WHT = I`
+4. **Codebook Correctness**: Verify centroids match Lloyd-Max for N(0, 1/128)
+5. **Metal vs CPU Parity**: Verify GPU and CPU produce identical results
+6. **Per-Layer Adaptive**: Verify sensitive layers use higher precision
+7. **Memory Bounds**: Verify no buffer overflows in bit packing
+
+### Recommended Test Suite
+```python
+# tests/test_polar_quant.py
+def test_roundtrip():
+    """Encode then decode should recover original within tolerance."""
+    
+def test_inner_product_preservation():
+    """Q·K dot product should be preserved through compression."""
+    
+def test_wht_orthogonality():
+    """WHT matrix should be orthogonal."""
+    
+def test_codebook_optimality():
+    """Centroids should minimize MSE for N(0, 1/128)."""
+```
+
+## Security Considerations
+
+### 1. Buffer Overflows
+- **Risk**: Bit packing/unpacking could overflow if dimension not power of 2
+- **Mitigation**: Static asserts in Metal shaders, runtime checks in CPU code
+- **Status**: ⚠️ Need verification
+
+### 2. Numerical Stability
+- **Risk**: Division by zero in `1.0 / (norm + 1e-9)`
+- **Mitigation**: Epsilon guard present
+- **Status**: ✅ Handled
+
+### 3. Memory Safety
+- **Risk**: C/C++ code has no bounds checking
+- **Mitigation**: Use Rust wrapper or sanitize inputs
+- **Status**: ⚠️ No safety wrapper
+
+### 4. Denial of Service
+- **Risk**: Maliciously crafted KV vectors could cause slow quantization
+- **Mitigation**: Fixed iteration count in Lloyd-Max search
+- **Status**: ✅ Bounded
+
+### 5. Side Channels
+- **Risk**: Timing differences in quantization could leak information
+- **Mitigation**: Constant-time implementation needed
+- **Status**: ❌ Not implemented
+
+## Dependencies
+
+### Build Dependencies
+- **CMake**: Build system
+- **Metal SDK**: GPU shaders (macOS)
+- **C++17**: Language standard
+
+### Runtime Dependencies
+- **Apple Silicon**: M1/M2/M3/M4
+- **macOS**: Metal GPU support
+- **llama.cpp**: Inference engine (forked)
+
+### External References
+- [TheTom/llama-cpp-turboquant](https://github.com/TheTom/llama-cpp-turboquant) — Primary fork
+- [TheTom/turboquant_plus](https://github.com/TheTom/turboquant_plus) — Reference implementation
+- [amirzandieh/QJL](https://github.com/amirzandieh/QJL) — QJL author's code
+- [rachittshah/mlx-turboquant](https://github.com/rachittshah/mlx-turboquant) — MLX fallback
+
+## Deployment
+
+### Build
+```bash
+cd llama-cpp-turboquant
+git checkout feature/turboquant-kv-cache
+cmake -B build -DGGML_METAL=ON -DCMAKE_BUILD_TYPE=Release
+cmake --build build -j$(sysctl -n hw.ncpu)
+```
+
+### Run
+```bash
+export TURBO_LAYER_ADAPTIVE=7
+./build/bin/llama-server \
+  -m /path/to/model.gguf \
+  --port 11434 \
+  -ctk turbo4 -ctv turbo4 \
+  -c 131072
+```
+
+### Validate
+```bash
+curl http://localhost:11434/v1/chat/completions \
+  -H "Content-Type: application/json" \
+  -d '{"model":"qwen3.5","messages":[{"role":"user","content":"hello"}]}'
+```
+
+## Open Questions
+
+1. **QJL Status**: Infrastructure exists but is disabled. When will it be needed?
+2. **Upstream Landing**: When will TurboQuant be merged into llama.cpp mainline?
+3. **Quality Threshold**: What PPL delta is acceptable for production use?
+4. **Multi-GPU**: Does TurboQuant work with tensor parallelism?
+
+## Changelog
+
+- **2026-03-30**: Phase 1 complete. PolarQuant MVP verified. 73% KV savings confirmed.
+- **2026-04-14**: GENOME.md generated. Test gaps identified. Security considerations documented.

tests/test_turboquant.py

@@ -0,0 +1,141 @@
+#!/usr/bin/env python3
+"""
+TurboQuant Test Suite
+Tests for critical paths in KV cache compression.
+
+Issue #679: Codebase Genome: turboquant — Full Analysis
+"""
+import unittest
+import subprocess
+import json
+import os
+import sys
+
+class TestTurboQuant(unittest.TestCase):
+    """Test TurboQuant implementation."""
+    
+    def test_repo_structure(self):
+        """Verify expected files exist."""
+        required_files = [
+            "llama-turbo.h",
+            "llama-turbo.cpp",
+            "ggml-metal-turbo.metal",
+            "README.md",
+            "GENOME.md"
+        ]
+        
+        for filename in required_files:
+            filepath = os.path.join(os.path.dirname(__file__), "..", filename)
+            self.assertTrue(os.path.exists(filepath), f"Missing required file: {filename}")
+    
+    def test_benchmarks_exist(self):
+        """Verify benchmark scripts exist."""
+        benchmark_files = [
+            "benchmarks/run_benchmarks.py",
+            "benchmarks/run_perplexity.py",
+            "benchmarks/run_long_session.py"
+        ]
+        
+        for filename in benchmark_files:
+            filepath = os.path.join(os.path.dirname(__file__), "..", filename)
+            self.assertTrue(os.path.exists(filepath), f"Missing benchmark file: {filename}")
+    
+    def test_docs_complete(self):
+        """Verify documentation exists."""
+        doc_files = [
+            "docs/PROJECT_STATUS.md",
+            "profiles/README.md"
+        ]
+        
+        for filename in doc_files:
+            filepath = os.path.join(os.path.dirname(__file__), "..", filename)
+            self.assertTrue(os.path.exists(filepath), f"Missing doc file: {filename}")
+    
+    def test_genome_generated(self):
+        """Verify GENOME.md was generated."""
+        genome_path = os.path.join(os.path.dirname(__file__), "..", "GENOME.md")
+        self.assertTrue(os.path.exists(genome_path), "GENOME.md not found")
+        
+        # Check it has required sections
+        with open(genome_path, 'r') as f:
+            content = f.read()
+        
+        required_sections = [
+            "## Project Overview",
+            "## Architecture",
+            "## Entry Points",
+            "## Data Flow",
+            "## Key Abstractions",
+            "## API Surface",
+            "## Test Coverage Gaps",
+            "## Security Considerations"
+        ]
+        
+        for section in required_sections:
+            self.assertIn(section, content, f"GENOME.md missing section: {section}")
+    
+    def test_metal_shader_syntax(self):
+        """Basic syntax check for Metal shader."""
+        shader_path = os.path.join(os.path.dirname(__file__), "..", "ggml-metal-turbo.metal")
+        with open(shader_path, 'r') as f:
+            content = f.read()
+        
+        # Check for key functions
+        self.assertIn("kernel_fwht_128", content, "Missing kernel_fwht_128 function")
+        self.assertIn("kernel_turbo4_dequant", content, "Missing kernel_turbo4_dequant function")
+        self.assertIn("turbo4_centroids", content, "Missing turbo4_centroids array")
+    
+    def test_cpp_header(self):
+        """Verify C++ header has correct declarations."""
+        header_path = os.path.join(os.path.dirname(__file__), "..", "llama-turbo.h")
+        with open(header_path, 'r') as f:
+            content = f.read()
+        
+        # Check for function declarations
+        self.assertIn("polar_quant_encode_turbo4", content, "Missing encode function")
+        self.assertIn("polar_quant_decode_turbo4", content, "Missing decode function")
+        self.assertIn('extern "C"', content, "Missing C linkage")
+
+class TestBenchmarks(unittest.TestCase):
+    """Test benchmark infrastructure."""
+    
+    def test_benchmark_imports(self):
+        """Verify benchmark script can be imported."""
+        benchmark_path = os.path.join(os.path.dirname(__file__), "..", "benchmarks", "run_benchmarks.py")
+        
+        # Check file exists
+        self.assertTrue(os.path.exists(benchmark_path), "Benchmark script not found")
+        
+        # Check it has main function
+        with open(benchmark_path, 'r') as f:
+            content = f.read()
+        
+        self.assertIn("def main():", content, "Benchmark script missing main function")
+        self.assertIn("argparse", content, "Benchmark script missing argparse")
+
+class TestDocumentation(unittest.TestCase):
+    """Test documentation completeness."""
+    
+    def test_readme_sections(self):
+        """Verify README has required sections."""
+        readme_path = os.path.join(os.path.dirname(__file__), "..", "README.md")
+        with open(readme_path, 'r') as f:
+            content = f.read()
+        
+        required_sections = ["## What", "## Why", "## Status", "## Roles"]
+        for section in required_sections:
+            self.assertIn(section, content, f"README missing section: {section}")
+    
+    def test_project_status_sections(self):
+        """Verify PROJECT_STATUS.md has required sections."""
+        status_path = os.path.join(os.path.dirname(__file__), "..", "docs", "PROJECT_STATUS.md")
+        with open(status_path, 'r') as f:
+            content = f.read()
+        
+        # Check for key findings
+        self.assertIn("73%", content, "Missing 73% savings metric")
+        self.assertIn("PolarQuant", content, "Missing PolarQuant references")
+        self.assertIn("Metal", content, "Missing Metal shader references")
+
+if __name__ == "__main__":
+    unittest.main()