Reorganize repository structure and remove redundant files

- Moved generate_figures.py and consolidate_model_results.py to code/ folder
- Removed redundant visualization scripts that duplicate toolbox functionality:
  - all_losses.py, stripplot.py, oz_losses.py (duplicate llm_stylometry.visualization)
  - loss_heatmaps.py (duplicate of heatmaps.py)
  - confusion_matrix.py (not used in paper)
  - t_test_figs.py (duplicate of t_tests.py)
- Updated run_llm_stylometry.sh to use new paths
- Updated README to reflect new structure with code/ containing CLI and training scripts
- Kept only essential training scripts in code/ folder

Author: jeremymanning

README.md

@@ -21,6 +21,12 @@ llm-stylometry/
 │   ├── utils/          # Helper utilities
 │   ├── visualization/  # Plotting and visualization
 │   └── cli_utils.py    # CLI helper functions
+├── code/                # Training and CLI scripts
+│   ├── generate_figures.py       # Main CLI entry point
+│   ├── consolidate_model_results.py # Result consolidation
+│   ├── main.py         # Model training orchestration
+│   ├── clean.py        # Data preprocessing
+│   └── ...             # Supporting training modules
 ├── data/                # Datasets and results
 │   ├── raw/            # Original texts from Project Gutenberg
 │   ├── cleaned/        # Preprocessed texts by author
@@ -35,8 +41,6 @@ llm-stylometry/
 │   ├── data/           # Test data and fixtures
 │   ├── test_*.py       # Test modules
 │   └── check_outputs.py # Output validation script
-├── consolidate_model_results.py # Consolidate training results
-├── generate_figures.py  # Main CLI entry point
 ├── run_llm_stylometry.sh # Shell wrapper for easy setup
 ├── LICENSE             # MIT License
 ├── README.md           # This file

code/all_losses.py

@@ -52,7 +52,7 @@ def train_models():
 
     # Consolidate results
     safe_print("\nConsolidating model results...")
-    result = subprocess.run([sys.executable, 'consolidate_model_results.py'], capture_output=True)
+    result = subprocess.run([sys.executable, 'code/consolidate_model_results.py'], capture_output=True)
     if result.returncode != 0:
         safe_print(f"Error consolidating results: {result.stderr.decode()}")
         return False