docs: update TODO.md with Phase 12 completion and v0.9.1 status

Phase 12 Accomplishments:
- Test Coverage: 26% → 84% overall (513 new tests for git modules)
- Code Duplication: 15-20% → <5% (navigation/shared.py centralization)
- Decorator Migration: 100% consistency (51 modules using _decorators.py)
- Documentation: ~5,000 lines across 11 files (ARCHITECTURE.md, examples, etc.)

Current Status (v0.9.1):
- 1,775 tests passing, 84% coverage
- 461+ functions across 15+ modules
- 100% ruff and mypy compliance
- Production-ready documentation

Next Priorities:
- CI/CD Enhancements (RECOMMENDED)
- Performance Optimization
- Additional Language Support

Compacted Phase 1-9 details for brevity while maintaining accuracy.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: jwesleye

TODO.md

@@ -1,162 +1,175 @@
 # Coding Open Agent Tools - TODO
 
-**Current Version**: v0.5.0
-**Last Updated**: 2025-11-07
-
-## ✅ Completed Phases
-
-### Phase 1-3: Repository Setup & Module Migration (v0.1.0-beta, v0.1.1)
-- [x] All 38 functions migrated from basic-open-agent-tools
-- [x] Analysis module (14 functions)
-- [x] Git module (9 functions)
-- [x] Profiling module (8 functions)
-- [x] Quality module (7 functions)
-- [x] GitHub infrastructure (issue templates, workflows, automation)
-- [x] 170 tests, 82% coverage, 100% ruff/mypy compliance
-- [x] Published to PyPI
-
-### Phase 4-5: Shell & Python Modules (v0.2.0) - ✅ COMPLETED
-- [x] **Shell Module** (13 functions): validators, security, formatters, parsers, analyzers
-- [x] **Python Module** (15 functions): validators, extractors, formatters, analyzers
-- [x] Enhanced secret scanning with detect-secrets (optional dependency)
-- [x] 271 new tests added (451 total)
-- [x] Code coverage: 86% overall
-- [x] 100% ruff and mypy compliance maintained
-
-### Phase 6: Database Module (v0.3.0-v0.3.4) - ✅ COMPLETED
-- [x] **Database Module** (18 functions): operations, schema, query builders, utils
-- [x] SQLite operations with pure stdlib (zero dependencies)
-- [x] Safe query building to prevent SQL injection
-- [x] Centralized STDLIB_MODULES constant
-- [x] Enhanced helpers.py with tool introspection utilities
-- [x] 570 total tests, 86% coverage maintained
-- [x] Fixed Pydantic validation issues in helper functions
-
-### Phase 7: Git Enhancement Module (v0.3.5) - ✅ COMPLETED
-- [x] **Git Enhancement Module** (70 functions added to git module)
-- [x] 11 subcategories: commits, hooks, config, health, conflicts, security, submodules, workflows, remotes, tags, diffs
-- [x] Commit message validation with conventional commits
-- [x] Git hooks management and testing
-- [x] Repository health analysis (large files, staleness)
-- [x] Security auditing (secrets, signatures)
-- [x] Workflow validation (gitflow, trunk-based)
-- [x] 570 total tests passing
-- [x] Deprecated @adk_tool decorator (non-existent import)
-- [x] Updated to @strands_tool only (Google ADK uses standard callables)
-
-### Phase 8: Python Navigation Module (v0.4.4) - ✅ COMPLETED
-- [x] **Python Navigation Functions** (10 functions added to python module)
-- [x] Token-saving code exploration tools (85-95% reduction)
-- [x] Line number extraction for targeted Read operations
-- [x] Module overviews, function/class listings
-- [x] Signature and docstring extraction
-- [x] Public API identification
-- [x] 53 comprehensive tests (84% coverage)
-- [x] 100% ruff and mypy compliance maintained
-
-### Phase 9: Python Navigation Extensions (v0.5.0) - ✅ COMPLETED
-- [x] **Python Navigation Advanced Functions** (7 functions added to python module)
-- [x] Function body extraction without full file reads (80-90% token savings)
-- [x] Function call analysis (what does a function call?)
-- [x] Usage analysis (where is a function used?)
-- [x] Method-specific line numbers in classes
-- [x] Class hierarchy and inheritance inspection
-- [x] Decorator-based definition search (@tool, @property, etc.)
-- [x] Class docstring extraction
-- [x] 22 comprehensive tests (75 total navigation tests)
-- [x] 100% ruff and mypy compliance maintained
-
-### Current Status (v0.5.0) ✅ RELEASED
-- **Total Functions**: 171 across 7 modules (17 navigation tools!)
-- **Total Tests**: 645 passing (+22 new tests)
-- **Code Coverage**: Maintained quality standards (80%+)
-- **Code Quality**: 100% ruff and mypy --strict compliance
-- **Modules**: analysis (14), git (79), profiling (8), quality (7), shell (13), python (32), database (18)
-- **Decorator Pattern**: @strands_tool only (ADK works with standard callables)
+**Current Version**: v0.9.1
+**Last Updated**: 2025-11-24
+
+## ✅ Completed Phases (Compacted)
+
+### Phase 1-9: Foundation & Core Modules (v0.1.0 - v0.5.0) - ✅ COMPLETED
+- [x] Repository setup, module migration, GitHub infrastructure
+- [x] Analysis module (14 functions), Git module (79 functions)
+- [x] Profiling module (8 functions), Quality module (7 functions)
+- [x] Shell module (13 functions), Python module (32 functions including 17 navigation tools)
+- [x] Database module (18 functions with pure stdlib SQLite)
+- [x] 645 tests passing, 80%+ coverage, 100% ruff/mypy compliance
+- [x] Published to PyPI, @strands_tool decorator pattern established
+
+### Phase 10: Multi-Language Navigation (v0.6.0-v0.9.0) - ✅ COMPLETED
+- [x] **Navigation Modules** (8 languages): C++, C#, Go, Java, JavaScript, Python, Ruby, Rust
+- [x] 184 navigation functions total (23 functions per language)
+- [x] Tree-sitter integration with graceful fallback
+- [x] Token savings: 70-95% reduction vs reading full files
+- [x] 526 navigation tests passing, 68-88% coverage per module
+
+### Phase 11: Configuration Modules (v0.8.0-v0.9.0) - ✅ COMPLETED
+- [x] **Config Module** (6 submodules, 42 functions total)
+- [x] Submodules: best_practices, env, extraction, formats, security, validation
+- [x] YAML/TOML/JSON parsing and validation
+- [x] Secret detection and security scanning
+- [x] Environment variable management
+- [x] Configuration best practices checking
+- [x] Full Windows compatibility
+
+### Phase 12: Code Quality & Documentation (v0.9.1) - ✅ COMPLETED (2025-11-24)
+- [x] **Test Coverage Expansion**: 26% → 84% overall coverage
+  - Added 513 new tests for 11 git modules (health, security, commits, conflicts, hooks, diffs, config, remotes, workflows, tags, submodules)
+  - All git modules now at 80-93% coverage
+  - Fixed 18 failing tests
+- [x] **Code Duplication Reduction**: 15-20% → <5%
+  - Created navigation/shared.py with centralized utilities
+  - Refactored all 8 navigation modules
+  - Eliminated 335 lines of duplicated code
+- [x] **Decorator Migration**: 100% consistency
+  - Migrated 14 modules to centralized _decorators.py pattern
+  - All 51 modules now use consistent decorator imports
+- [x] **Comprehensive Documentation Suite**
+  - ARCHITECTURE.md (575 lines): System design, patterns, standards
+  - CONTRIBUTING.md (535 lines): Development workflow, quality standards
+  - docs/GETTING_STARTED.md (345 lines): Installation and quick start
+  - docs/DOCUMENTATION_INDEX.md (330 lines): Complete navigation
+  - docs/examples/ (6 files): Runnable examples with token savings analysis
+  - Total: ~5,000 lines of documentation
+
+### Current Status (v0.9.1) ✅ LATEST
+- **Total Functions**: 461+ across 15+ modules
+- **Total Tests**: 1,775 passing
+- **Code Coverage**: 84% overall (83% for navigation modules)
+- **Code Quality**: 100% ruff and mypy compliance
+- **Code Duplication**: <5% (reduced from 15-20%)
+- **Documentation**: Production-ready with comprehensive examples
+- **Modules**:
+  - Core: analysis (14), git (79), profiling (8), quality (7), database (18), helpers
+  - Languages: shell (13), python (32), config (42)
+  - Navigation: cpp, csharp, go, java, javascript, python, ruby, rust (184 total)
+  - Shared: navigation/shared (5 utilities)
+- **Decorator Pattern**: @strands_tool only (ADK/LangGraph work with standard callables)
 - **Published**: PyPI package available
 
 ---
 
-## 🚀 Upcoming Modules (Roadmap v3.0)
+## 🚀 Next Priorities
 
-### v0.6.0 - Configuration Validation Module (10 functions)
+### Option 1: CI/CD Enhancements (RECOMMENDED)
 **Priority**: High
+**Effort**: Low-Medium (2-3 hours)
 
-- [ ] Validators: YAML/TOML/JSON syntax, schema validation, CI config
-- [ ] Security: scan for secrets (detect-secrets), insecure settings
-- [ ] Analyzers: dependency conflicts, version constraints
+- [ ] GitHub Actions workflow for automated testing
+- [ ] Coverage reporting (Codecov/Coveralls)
+- [ ] Automated linting and type checking on PRs
+- [ ] Pre-commit hooks configuration
+- [ ] Release automation workflow
+- [ ] Update main README.md with badges and quick start
 
-### v0.6.0+ - See ROADMAP.md
-Complete roadmap with 36 total modules through v1.0.0
+**Benefits**: Automated quality gates, prevent regressions, professional appearance
+
+### Option 2: Performance Optimization
+**Priority**: Medium
+**Effort**: Medium-High
+
+- [ ] Profile hot paths in navigation modules
+- [ ] Cache tree-sitter parsers for reuse
+- [ ] Optimize regex operations in analysis modules
+- [ ] Add memoization for expensive operations
+- [ ] Benchmark token savings with real-world scenarios
+
+### Option 3: Additional Language Support
+**Priority**: Low-Medium
+**Effort**: High per language
+
+- [ ] TypeScript navigation module (23 functions)
+- [ ] Kotlin navigation module (23 functions)
+- [ ] Swift navigation module (23 functions)
+- [ ] PHP navigation module (23 functions)
+
+### Option 4: Advanced Features
+**Priority**: Variable
+**Effort**: High per module
+
+- [ ] Git merge conflict resolution suggestions
+- [ ] Advanced code complexity metrics
+- [ ] Dependency graph analysis
+- [ ] Performance profiling integration
 
 ---
 
 ## 📊 Quality Metrics & Standards
 
 ### Maintained Standards
-- ✅ **Test Coverage**: 80%+ (currently 86%)
+- ✅ **Test Coverage**: 80%+ (currently 84%)
 - ✅ **Ruff Compliance**: 100% (linting + formatting)
 - ✅ **Mypy Compliance**: 100% (strict mode)
 - ✅ **Google ADK Compliance**: All functions
-- ✅ **Documentation**: Comprehensive docstrings
-
-### Testing Requirements (Per Module)
-- Unit tests for all functions
-- Error handling tests (TypeError, ValueError)
-- Integration tests where applicable
-- Edge case coverage
-- 80%+ coverage per file
+- ✅ **Documentation**: Comprehensive with examples
+- ✅ **Code Duplication**: <5%
 
 ### Code Quality Checklist (Per Release)
-- [ ] All ruff checks pass (`uv run ruff check src --fix`)
-- [ ] All ruff formatting applied (`uv run ruff format src`)
-- [ ] All mypy checks pass (`uv run mypy src`)
-- [ ] All tests pass (`uv run pytest`)
-- [ ] Coverage ≥ 80% overall
-- [ ] Documentation updated (README, ROADMAP, CHANGELOG, TODO)
-- [ ] Version numbers consistent (pyproject.toml, __init__.py)
+- [x] All ruff checks pass (`uv run ruff check src --fix`)
+- [x] All ruff formatting applied (`uv run ruff format src`)
+- [x] All mypy checks pass (`uv run mypy src`)
+- [x] All tests pass (`uv run pytest`) - 1,775 tests passing
+- [x] Coverage ≥ 80% overall (currently 84%)
+- [x] Documentation updated (README, ARCHITECTURE, TODO)
+- [x] Version numbers consistent
 
 ---
 
 ## 📝 Documentation Maintenance
 
 ### Core Documents
 - [x] README.md - Project overview, installation, usage
-- [x] ROADMAP.md - Development roadmap (36 modules)
+- [x] ARCHITECTURE.md - System design and patterns (NEW)
+- [x] CONTRIBUTING.md - Development workflow (ENHANCED)
+- [x] docs/GETTING_STARTED.md - Quick start guide (NEW)
+- [x] docs/DOCUMENTATION_INDEX.md - Navigation (NEW)
+- [x] docs/examples/ - Runnable examples (NEW)
 - [x] CHANGELOG.md - Version history
-- [x] TODO.md - This file
-- [x] CONTRIBUTING.md - Contribution guidelines
+- [x] TODO.md - This file (UPDATED)
 - [x] SECURITY.md - Security policy
 - [x] CODE_OF_CONDUCT.md - Community standards
 
-### Module Documentation (Per Module)
-- Docstrings for all functions (Google style)
-- Type hints for all parameters and returns
-- Usage examples in docstrings
-- Error cases documented (Raises section)
-
-### Keep Updated
-- Version numbers across all docs
-- Function counts in README and ROADMAP
-- Test coverage statistics
-- Module status (planned → completed)
+### Documentation Quality
+- Complete architecture documentation with design patterns
+- Comprehensive contributing guidelines with code examples
+- 5 practical runnable examples demonstrating 70-95% token savings
+- Full navigation structure with module organization
+- Production-ready for user and contributor onboarding
 
 ---
 
 ## 🔄 Release Process Checklist
 
 ### Pre-Release (Cleanup)
-- [ ] Run `/cleanup` slash command
-- [ ] Fix all ruff/mypy errors
-- [ ] Ensure all tests pass
-- [ ] Update documentation
+- [x] Run `/cleanup` slash command (completed 2025-11-24)
+- [x] Fix all ruff/mypy errors
+- [x] Ensure all tests pass
+- [x] Update documentation
 
-### Version Bump
+### Version Bump (Next Release)
 - [ ] Update version in pyproject.toml
 - [ ] Update version in src/coding_open_agent_tools/__init__.py
 - [ ] Update CHANGELOG.md with release notes
 - [ ] Update TODO.md with completion status
-- [ ] Update README.md function counts if changed
+- [ ] Update README.md if needed
 
 ### Release
 - [ ] Commit version changes
@@ -173,19 +186,32 @@ Complete roadmap with 36 total modules through v1.0.0
 coding-open-agent-tools/
 ├── src/coding_open_agent_tools/
 │   ├── __init__.py (exports all modules)
+│   ├── _decorators.py (@strands_tool decorator)
+│   ├── navigation/
+│   │   ├── shared.py (5 shared utilities - NEW)
 │   ├── analysis/ (14 functions)
-│   ├── git/ (79 functions - ENHANCED)
+│   ├── git/ (79 functions in 14 submodules)
+│   │   ├── health.py, security.py, commits.py, conflicts.py
+│   │   ├── hooks.py, diffs.py, config.py, remotes.py
+│   │   ├── workflows.py, tags.py, submodules.py, etc.
 │   ├── profiling/ (8 functions)
 │   ├── quality/ (7 functions)
 │   ├── shell/ (13 functions)
-│   ├── python/ (32 functions - 17 navigation tools!)
+│   ├── python/ (32 functions)
+│   ├── config/ (42 functions in 6 submodules)
 │   ├── database/ (18 functions)
-│   ├── helpers.py (tool loading utilities)
-│   ├── exceptions.py (common exceptions)
-│   ├── _decorators.py (@strands_tool decorator)
-│   └── types.py (shared types)
-├── tests/ (645 tests, 80%+ coverage)
-├── docs/ (ROADMAP, MODULE_SUMMARY, PRD)
+│   ├── [language]/navigation.py (8 languages × 23 functions each)
+│   │   ├── cpp, csharp, go, java, javascript, ruby, rust
+│   ├── helpers.py, exceptions.py, types.py
+├── tests/ (1,775 tests, 84% coverage)
+│   ├── git/ (571 tests - 11 modules with comprehensive coverage)
+│   ├── [language]/ (526 navigation tests across 8 languages)
+│   └── [other modules]
+├── docs/ (NEW - comprehensive documentation)
+│   ├── ARCHITECTURE.md, GETTING_STARTED.md
+│   ├── DOCUMENTATION_INDEX.md, DOCUMENTATION_SUMMARY.md
+│   ├── examples/ (5 runnable scripts + README)
+├── CONTRIBUTING.md (ENHANCED)
 └── [config files]
 ```
 
@@ -199,6 +225,7 @@ coding-open-agent-tools/
 - ✅ Extractors - Pull specific data
 - ✅ Formatters - Apply deterministic rules
 - ✅ Scanners - Rule-based pattern detection
+- ✅ Navigators - Explore code without reading full files (70-95% token savings)
 
 **NOT Building** (Agents already excel):
 - ❌ Code generators
@@ -208,7 +235,7 @@ coding-open-agent-tools/
 
 ---
 
-**Document Version**: 5.0
-**Status**: Active Development - v0.5.0 Released
-**Next Milestone**: v0.6.0 Release (Configuration Validation Module)
-**Future**: See ROADMAP.md for complete 36-module plan through v1.0.0
+**Document Version**: 9.1
+**Status**: Production Ready - v0.9.1
+**Next Milestone**: CI/CD Automation + README Enhancement
+**Quality Score**: Excellent (84% coverage, 100% compliance, <5% duplication)