feat: Phase 5 complete - Production-ready release

- Safety gates with Tree-Sitter validation
- Self-healing retry loops
- Beautiful CLI with Typer and Rich
- Complete provenance logging
- Organized documentation
- Added CONTRIBUTING.md and CHANGELOG.md
- Cleaned up all temporary files

All 5 phases complete. Ready for production use.

Author: vivek5200

.gitignore

@@ -9,6 +9,7 @@ venv_old/
 env/
 ENV/
 .venv
+*.pyc
 
 # Neo4j
 neo4j_data/
@@ -25,12 +26,26 @@ neo4j_logs/
 
 # Logs
 *.log
+ouroboros_generation.log
 
-# Test artifacts
+# Test artifacts and temporary files
 tests/synthetic_benchmarks/output/
-artifact_metadata.json
+artifacts/*.json
+artifact_metadata*.json
+test_*.py
+*.backup
+temp_*.py
 
-# Interim reports (consolidated into PHASE1_COMPLETE.md)
+# Interim reports (consolidated)
 TASK1_VALIDATION.md
 TASK2_REPORT.md
 TASK3_SUMMARY.md
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Pytest
+.pytest_cache/
+.coverage
+htmlcov/

CHANGELOG.md

@@ -0,0 +1,204 @@
+# Changelog
+
+All notable changes to Ouroboros will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [2.0.0] - 2025-12-21
+
+### Added - Phase 5: The Integration Loop 🎉
+
+#### Safety Gate
+- Tree-Sitter syntax validator for Python, JavaScript, TypeScript
+- Automatic syntax validation before any code touches disk
+- Detailed error reporting with line numbers and context
+- Self-healing retry loop (up to 3 attempts with error feedback)
+- Configurable safety gate enable/disable
+
+#### CLI
+- Beautiful CLI using Typer and Rich libraries
+- `refactor` command - Generate and apply code patches
+- `status` command - Check run status and provenance
+- `list-runs` command - View recent generation runs
+- Progress bars and spinners for long operations
+- Rich table output for results
+- Dry-run mode to preview changes
+- Auto-apply for low-risk patches
+- Risk scoring (0.0-1.0) for all patches
+- Windows (`ouroboros.bat`) and Unix (`ouroboros.sh`) launchers
+
+#### Provenance Logging
+- Complete audit trail for every generation run
+- Model usage tracking (Reasoner, Compressor, Generator)
+- Safety check logging with timestamps
+- File modification tracking with SHA256 hashes
+- JSON export to `artifact_metadata.json`
+- Metadata includes: run_id, models_used, safety_checks, file_modifications
+
+#### Builder Enhancements
+- Integrated syntax validator into generation pipeline
+- Retry mechanism with enhanced error feedback
+- Validation result tracking in metadata
+- Configurable max retry attempts
+
+#### Pipeline Integration
+- Provenance logger initialized for every run
+- Model usage tracked across all phases
+- Safety checks logged after generation
+- File modifications tracked on apply
+- Error logging with failure provenance
+
+#### Documentation
+- `PHASE_5_COMPLETE.md` - Comprehensive Phase 5 guide
+- `CLI_QUICK_REFERENCE.md` - Quick CLI reference
+- `PHASE_5_SUMMARY.md` - Implementation summary
+- Updated main `README.md` with Phase 5 info
+- `CONTRIBUTING.md` - Contribution guidelines
+- `CHANGELOG.md` - This file
+
+#### Dependencies
+- Added `typer>=0.9.0` for CLI framework
+- Added `rich>=13.7.0` for beautiful terminal output
+- Added `click>=8.1.0` as typer dependency
+
+### Changed
+- Updated `.gitignore` to ignore test files and artifacts
+- Moved all documentation to `docs/` folder
+- Updated `README.md` with new project structure
+- Enhanced error handling across all components
+
+### Fixed
+- Builder now validates syntax before applying changes
+- Proper error context in validation failures
+- Provenance saved even on generation failures
+
+## [1.5.0] - 2025-12-10
+
+### Added - Phase 4: The Builder
+
+#### Discrete Diffusion
+- Discrete diffusion model for code generation
+- Cosine noise schedule (1000 steps)
+- Classifier-free guidance (CFG scale 7.5)
+- Temperature control for generation
+- Multiple backbone support (Mock, GPT, Claude)
+
+#### Builder Component
+- High-level orchestrator for code generation
+- Batch patch generation
+- Risk scoring for patches
+- Unified diff generation
+- Provenance metadata tracking
+
+#### AST Masking
+- Tree-sitter based AST masking
+- Target-specific function/class masking
+- Masked span tracking
+- Multi-language support
+
+#### Configuration
+- Fast mode (10 steps)
+- Balanced mode (50 steps)
+- Quality mode (100 steps)
+- Mock mode for testing
+
+#### Documentation
+- `PHASE_4_COMPLETE.md` - Complete Phase 4 documentation
+- Architecture diagrams
+- Usage examples
+- API reference
+
+### Changed
+- Refactored generation pipeline
+- Enhanced metadata tracking
+- Improved error handling
+
+## [1.0.0] - 2025-12-08
+
+### Added - Phase 1: The Librarian
+
+#### Knowledge Graph
+- Neo4j graph database integration
+- Tree-sitter code parsing (Python, JS, TS)
+- Provenance metadata tracking
+- Code checksum validation
+
+#### Graph Construction
+- File node creation
+- Function/class node extraction
+- Dependency relationship mapping
+- Import tracking
+
+#### Retrieval
+- Graph traversal queries
+- Context extraction
+- Related node discovery
+
+#### Infrastructure
+- Docker Compose setup for Neo4j
+- Database schema initialization
+- Ingestion pipeline
+- Synthetic benchmarks
+
+### Added - Phase 2: The Reasoner
+
+#### Dependency Analysis
+- Code dependency tracking
+- Impact assessment
+- Change propagation analysis
+
+#### LLM Integration
+- Claude 3.5 Sonnet support
+- GPT-4 support
+- Anthropic API client
+- Plan generation
+
+### Added - Phase 3: The Compressor
+
+#### Context Encoding
+- AI21 Jamba 1.5 Mini integration
+- 256k token context window
+- Context compression
+- Token optimization
+
+#### Configuration
+- AI21 API setup
+- Compression parameters
+- Validation pipeline
+
+### Infrastructure
+- Python 3.10+ support
+- Virtual environment setup
+- Requirements management
+- Environment variables (.env)
+
+## [Unreleased]
+
+### Planned Features
+- Semantic validation (beyond syntax)
+- Security scanning
+- Performance profiling
+- Web UI
+- VS Code extension
+- GitHub Actions integration
+- CI/CD pipeline
+- Additional language support
+- Improved retry strategies
+- Rollback automation
+
+---
+
+## Version History
+
+- **v2.0.0** (Dec 21, 2025) - Phase 5: Integration Loop (Safety, CLI, Provenance)
+- **v1.5.0** (Dec 10, 2025) - Phase 4: The Builder (Discrete Diffusion)
+- **v1.0.0** (Dec 08, 2025) - Phase 1-3: Foundation (Graph, Reasoner, Compressor)
+
+## Contributing
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) for contribution guidelines.
+
+## License
+
+MIT License - see [LICENSE](LICENSE) for details.