Merge refactor/v0.7.0: Complete repository organization

Complete codebase reorganization from flat structure (45 files at root)
to organized directory structure (9 directories):
- src/ - Core implementation modules
- training/ - Training infrastructure
- tools/ - Development utilities
- tests/ - Test suite
- obsolete/ - Preserved historical files
- docs/ - Portfolio documentation
- artifacts/ - Training artifacts (models, checkpoints, data, reports)
- data/ - Game data (PGN files organized by opponent)
- logs/ - Build and test logs

All functionality preserved, tests passing (24/24), zero data loss.
Tournament submission (my_agent.py) unaffected and verified functional.
Root directory: 45 files → 9 committed files (clean structure achieved).

Author: LeonByte

.dockerignore

@@ -45,10 +45,10 @@ phase4_checkpoints/
 logs/
 runs/
 
-# Test files (exclude future test files, but Phase 2 tests are needed in Docker)
+# Test files (v0.7.0: tests/ directory now included in Docker)
 # test_*.py  # COMMENTED: Blocking test_phase2.py - keep this commented during Phase 2-6
 *_test.py
-tests/
+# tests/  # REMOVED: tests/ directory now part of organized structure
 
 # Phase test files needed in Docker:
 # - test_phase2.py (Phase 2 validation)
@@ -91,4 +91,11 @@ __MACOSX/
 .cache/
 
 # Debug scripts (not needed in container)
-debug_*.py
+debug_*.py
+
+# Phase 7.12: Organized artifact directories (v0.7.0)
+# These directories contain training artifacts, game data, and logs
+# Not needed in Docker container - keeps image lean
+artifacts/
+data/
+logs/

.gitignore

@@ -234,6 +234,7 @@ best_checkpoint.pkl
 test_*.pkl
 test_*.npy
 
-# ELO measurement files (can regenerate)
-baseline_elo_measurement.json
+# Performance reports and measurements (generated artifacts - can regenerate)
+*_report.json
+*_measurement.json
 elo_measurement_*.pgn

.refactor_baseline.txt

@@ -0,0 +1,19 @@
+v0.7.0 Refactoring Baseline (Oct 16, 2025)
+==========================================
+
+Starting Point: v0.6.0 (Phase 6 Complete, Tournament Ready)
+
+Current Structure:
+- 91 total items at root directory
+- 45+ Python files at root level  
+- Only organized directory: docs/
+
+Validation Status:
+- Docker image: neuraltactics (14.4GB)
+- test_phase5.py: 24/24 passing ✅
+- my_agent.py: Functional ✅
+- Tournament ready: Yes ✅
+
+Target: Organize into src/, training/, tools/, tests/, obsolete/
+Timeline: 5-6 hours (11 phases)
+Zero data loss: All files will be preserved

Dockerfile

@@ -1,59 +1,26 @@
 FROM python:3.9-slim
 
 WORKDIR /app
+
+# Set Python path to include /app for module imports
+ENV PYTHONPATH=/app
+
+# Install dependencies
 COPY requirements.txt .
 RUN pip install -r requirements.txt
 
-# Copy tournament infrastructure
+# Copy tournament interface and submission
 COPY agent_interface.py .
-COPY game_driver.py .
-COPY random_agent.py .
-COPY greedy_agent.py .
-
-# Copy student agent and Phase 2 modules
 COPY my_agent.py .
-COPY chess_state.py .
-COPY evaluation.py .
-COPY test_phase2.py .
-
-# Copy Phase 3 modules
-COPY training.py .
-COPY nnue_network.py .
-COPY nnue_integration.py .
-COPY test_phase3.py .
-COPY my_agent_phase3_demo.py .
-COPY my_agent_tournament.py .
-
-# Copy Phase 4 modules
-COPY phase4_training_pipeline.py .
-COPY checkpoint_manager.py .
-COPY training_metrics.py .
-COPY hyperparameter_optimizer.py .
-COPY performance_profiler.py .
-COPY advanced_training.py .
-COPY test_phase4.py .
-COPY validate_phase4.py .
-COPY quick_validate_phase4.py .
-
-# Copy Phase 5 modules
-COPY tactical_patterns.py .
-COPY test_tactical_patterns.py .
-COPY endgame_mastery.py .
-COPY test_endgame_mastery.py .
-COPY middlegame_strategy.py .
-COPY test_middlegame_strategy.py .
-COPY opening_repertoire.py .
-COPY test_opening_repertoire.py .
-COPY dynamic_evaluation.py .
-COPY test_dynamic_evaluation.py .
-COPY test_phase5.py .
 
-# Copy Phase 6 profiling and validation tools
-COPY profile_agent.py .
-COPY tournament_validation.py .
+# Copy organized directories
+COPY src/ src/
+COPY training/ training/
+COPY tools/ tools/
+COPY tests/ tests/
 
 # Set memory limits
 RUN ulimit -v 2000000  # 2GB memory limit
 
 # Default command
-CMD ["python", "game_driver.py"]
+CMD ["python", "tools/game_driver.py"]

README.md

@@ -18,10 +18,10 @@ Achieved ~2900 ELO through NNUE neural network training and strategic enhancemen
 docker build -t neuraltactics .
 
 # Run a game
-docker run neuraltactics python game_driver.py
+docker run neuraltactics python tools/game_driver.py
 
 # Run comprehensive tests
-docker run neuraltactics python test_phase5.py
+docker run neuraltactics python tests/test_phase5.py
 ```
 
 ## Key Features
@@ -65,23 +65,41 @@ Comprehensive technical documentation available in [`docs/`](./docs/):
 NeuralTactics/
 ├── 📄 README.md                # This file (quick start)
 ├── 📄 my_agent.py              # Tournament submission (3,168 lines)
+├── 📄 agent_interface.py       # Tournament interface
 ├── 📄 Dockerfile               # Tournament environment
 ├── 📄 requirements.txt         # Exact dependencies
+├── 📄 MIGRATION.md             # v0.6.0 → v0.7.0 migration guide
 │
-├── 📁 docs/                    # Comprehensive documentation
-│   ├── 📄 README.md            # Detailed overview
-│   ├── 📄 ARCHITECTURE.md      # Technical deep dive
-│   ├── 📄 TRAINING.md          # Training methodology
-│   ├── 📄 TOURNAMENT.md        # Compliance proof
-│   ├── 📄 RESULTS.md           # Performance analysis
-│   └── 📄 FAQ.md               # Compliance clarifications
+├── 📁 src/                     # Core implementation
+│   ├── 📁 state/               # Chess state representation
+│   ├── 📁 evaluation/          # Position evaluation (6 modules)
+│   └── 📁 neural/              # NNUE network implementation
 │
-├── 📄 game_driver.py           # Game runner
-├── 📄 random_agent.py          # Baseline opponent
-├── 📄 greedy_agent.py          # Baseline opponent
+├── 📁 training/                # Training infrastructure
+│   ├── 📄 trainer.py           # Main training loop
+│   ├── 📄 pipeline.py          # Optimized training pipeline
+│   └── 📄 metrics.py           # Performance tracking
 │
-├── 📄 test_phase5.py           # Comprehensive test suite (24 tests)
-└── 📄 tournament_validation.py # 100-game stress test
+├── 📁 tools/                   # Development utilities
+│   ├── 📄 game_driver.py       # Game runner
+│   ├── 📄 random_agent.py      # Baseline opponent
+│   └── 📄 greedy_agent.py      # Baseline opponent
+│
+├── 📁 tests/                   # Test suite
+│   ├── 📄 test_phase5.py       # Comprehensive tests (24 tests)
+│   └── 📄 tournament_validation.py # 100-game stress test
+│
+├── 📁 obsolete/                # Preserved historical files
+│   ├── 📄 my_agent_phase3_demo.py # Phase 3 demo (outdated)
+│   └── 📄 my_agent_tournament.py  # Sep 28 version (outdated)
+│
+└── 📁 docs/                    # Comprehensive documentation
+    ├── 📄 README.md            # Detailed overview
+    ├── 📄 ARCHITECTURE.md      # Technical deep dive
+    ├── 📄 TRAINING.md          # Training methodology
+    ├── 📄 TOURNAMENT.md        # Compliance proof
+    ├── 📄 RESULTS.md           # Performance analysis
+    └── 📄 FAQ.md               # Compliance clarifications
 ```
 
 
@@ -91,10 +109,10 @@ NeuralTactics/
 
 ```bash
 # Comprehensive test suite (24 tests)
-docker run neuraltactics python test_phase5.py
+docker run neuraltactics python tests/test_phase5.py
 
 # 100-game tournament validation
-docker run neuraltactics python tournament_validation.py
+docker run neuraltactics python tests/tournament_validation.py
 ```
 
 ### Local Development

artifacts/README.md

@@ -0,0 +1,43 @@
+# Artifacts Directory
+
+This directory contains training artifacts generated during development.
+
+## Structure
+
+```
+artifacts/
+├── models/              # Trained neural network models
+├── checkpoints/         # Training checkpoints
+├── training_data/       # Training datasets
+└── reports/             # Performance reports
+```
+
+## Contents
+
+### models/
+- `best_nnue_model.pth` - Best trained NNUE network weights
+- Neural network models saved during training
+
+### checkpoints/
+- `phase4_checkpoints/` - Phase 4 training checkpoints
+- `validation_checkpoints/` - Validation checkpoints
+- Intermediate training states for resuming training
+
+### training_data/
+- `training_data.pkl` - Complete training dataset (pickle format)
+- `training_positions.npy` - Position array for neural training
+- `training_outcomes.npy` - Outcome array for neural training
+- `training_progress.json` - Training progress metrics
+
+### reports/
+- `baseline_elo_measurement.json` - ELO measurement results
+- `phase4_performance_report.json` - Phase 4 performance metrics
+- Performance analysis reports
+
+## Note
+
+**These files are in `.gitignore` and `.dockerignore`.**
+- Not committed to repository (too large, binary files)
+- Not included in Docker images (not needed for tournament)
+- Generated locally during training and development
+- Excluded from portfolio presentation (show code, not artifacts)

data/README.md

@@ -0,0 +1,47 @@
+# Data Directory
+
+This directory contains game data generated during development and testing.
+
+## Structure
+
+```
+data/
+└── pgn_games/
+    ├── vs_greedy/       # Games against GreedyAgent
+    └── vs_random/       # Games against RandomAgent
+```
+
+## Contents
+
+### pgn_games/vs_greedy/
+- PGN files from ELO measurement games against GreedyAgent
+- Used for ELO rating calculation and performance analysis
+- 10 game files
+
+### pgn_games/vs_random/
+- PGN files from ELO measurement games against RandomAgent
+- Used for baseline performance comparison
+- 10 game files
+
+## PGN Format
+
+Each file contains a complete chess game in Portable Game Notation (PGN) format including:
+- Game metadata (players, date, result)
+- Move sequence
+- Game outcome
+
+## Usage
+
+These files can be analyzed for:
+- Game review and blunder analysis
+- Position evaluation debugging
+- Strategy effectiveness assessment
+- Training feedback loop
+
+## Note
+
+**These files are in `.gitignore` and `.dockerignore`.**
+- Not committed to repository (regenerated during testing)
+- Not included in Docker images (not needed for tournament)
+- Generated locally during ELO measurements
+- Can be regenerated by running tournament validation

docs/FAQ.md

@@ -263,7 +263,7 @@ docker run neuraltactics python training.py --generate-data --games 1000
 docker run neuraltactics python training.py --epochs 100 --batch-size 128 --lr 0.0008
 
 # Validate
-docker run neuraltactics python test_phase5.py
+docker run neuraltactics python tests/test_phase5.py
 ```
 
 ---

docs/README.md

@@ -34,20 +34,20 @@ NeuralTactics is a competitive chess AI developed for academic tournament play,
 docker build -t neuraltactics .
 
 # Play a game (agent vs RandomAgent)
-docker run neuraltactics python game_driver.py
+docker run neuraltactics python tools/game_driver.py
 
 # Run comprehensive test suite
-docker run neuraltactics python test_phase5.py
+docker run neuraltactics python tests/test_phase5.py
 ```
 
 ### Test Agent Performance
 
 ```bash
 # 100-game tournament validation
-docker run neuraltactics python tournament_validation.py
+docker run neuraltactics python tests/tournament_validation.py
 
 # Profile performance
-docker run neuraltactics python profile_agent.py
+docker run neuraltactics python tools/profile_agent.py
 ```
 
 ## Architecture Highlights
@@ -126,13 +126,19 @@ NeuralTactics/
 ├── 📄 requirements.txt         # Exact dependency versions
 ├── 📄 Dockerfile              # Tournament environment
 │
-├── 📄 game_driver.py          # Game runner and testing framework
-├── 📄 random_agent.py         # Baseline opponent (random moves)
-├── 📄 greedy_agent.py         # Baseline opponent (material greedy)
+├── 📁 src/                    # Core implementation (state, evaluation, neural)
+├── 📁 training/               # Training infrastructure
+├── 📁 tools/                  # Development utilities
+│   ├── 📄 game_driver.py      # Game runner and testing framework
+│   ├── 📄 random_agent.py     # Baseline opponent (random moves)
+│   └── 📄 greedy_agent.py     # Baseline opponent (material greedy)
 │
-├── 📄 test_phase5.py          # Comprehensive test suite (24 tests)
-├── 📄 tournament_validation.py # 100-game stress test
-├── 📄 profile_agent.py        # Performance profiling
+├── 📁 tests/                  # Test suite
+│   ├── 📄 test_phase5.py      # Comprehensive test suite (24 tests)
+│   ├── 📄 tournament_validation.py # 100-game stress test
+│   └── 📄 profile_agent.py    # Performance profiling
+│
+├── 📁 obsolete/               # Preserved historical files
 │
 └── 📁 docs/                   # Documentation
     ├── 📄 README.md           # This file (detailed overview)
@@ -147,7 +153,7 @@ NeuralTactics/
 
 ```bash
 # Phase 5 comprehensive validation (24 tests)
-docker run neuraltactics python test_phase5.py
+docker run neuraltactics python tests/test_phase5.py
 
 # Expected output: 24/24 tests passing
 # Coverage: Tactical, endgame, middlegame, opening, dynamic evaluation