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docs: reorganize documentation structure and add Phase 2 implementation
Major documentation reorganization following best practices: Documentation Organization: - Move PROJECT_GUIDE.md to docs/ for proper organization - Move ARCHITECTURE_DIAGRAM.md to docs/ for technical documentation - Move DEVELOPMENT_QUICKSTART.md to docs/ for developer resources - Preserve important claudedocs/ content in committed docs/ - logging_framework.md → docs/LOGGING.md - phase2_completion_report.md → docs/PHASE2_COMPLETION_REPORT.md - comprehensive_code_review.md → docs/CODE_REVIEW.md - Add docs/DOCUMENTATION_ORGANIZATION.md for organization rationale - Update .gitignore to exclude claudedocs/ (AI agent session context) Phase 2 Implementation (Complete): - Add cli_audit package with 11 modules (5,338 LOC) - Phase 2.1: Foundation (environment, config, package_managers, install_plan) - Phase 2.2: Core installation (installer with retry and validation) - Phase 2.3: Bulk operations (parallel installation with progress tracking) - Phase 2.4: Upgrade management (version comparison, breaking changes) - Phase 2.5: Reconciliation (multi-installation detection and management) - Phase 2.6: Logging framework (structured logging with console/file output) Testing Infrastructure: - Add comprehensive test suite (292 tests, 4,907 LOC) - Unit tests for all 11 Phase 2 modules - Integration tests for end-to-end workflows - Test fixtures for configuration validation Development Infrastructure: - Add CI/CD workflows (GitHub Actions) - ci.yml: Matrix testing (Python 3.10-3.12, Linux/macOS) - release.yml: Automated releases with PyPI publishing - dependabot.yml: Automated dependency updates - Add development tooling configuration - .flake8: Linting rules - mypy.ini: Type checking configuration - pytest.ini: Test configuration - pyproject.toml: Package metadata and dependencies - Add CONTRIBUTING.md with comprehensive contributor guide Documentation: - Add docs/PHASE2_API_REFERENCE.md (78 API symbols across 11 modules) - Add docs/phase2_api/environment.md (detailed module documentation) - Add docs/CODE_REVIEW.md (comprehensive quality assessment: 9.3/10) - Add docs/LOGGING.md (logging framework documentation) - Update README.md with Phase 2 features and code examples Quality: - Zero circular dependencies across 11 modules - Comprehensive type hints throughout - Frozen dataclasses for immutability - Thread-safe progress tracking - Retry logic with exponential backoff - Checksum verification for downloads - Breaking change detection and warnings - System tool safelist (26 protected tools) Cross-references updated in PHASE2_API_REFERENCE.md and environment.md to reflect new documentation locations. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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‎.flake8‎

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[flake8]
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max-line-length = 127
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extend-ignore = E203, W503
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exclude =
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.git,
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__pycache__,
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.venv,
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venv,
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build,
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dist,
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*.egg-info,
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.tox,
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.pytest_cache,
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node_modules
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# Error codes
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# E9: Runtime errors (syntax errors, indentation errors)
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# F63: Invalid print statement
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# F7: Syntax errors in type comments
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# F82: Undefined names in __all__
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per-file-ignores =
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__init__.py:F401
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tests/*:F401,F811

‎.github/dependabot.yml‎

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version: 2
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updates:
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# Python dependencies
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- package-ecosystem: "pip"
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directory: "/"
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schedule:
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interval: "weekly"
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day: "monday"
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open-pull-requests-limit: 10
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labels:
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- "dependencies"
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- "python"
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commit-message:
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prefix: "chore(deps)"
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include: "scope"
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# GitHub Actions
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"
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day: "monday"
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open-pull-requests-limit: 5
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labels:
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- "dependencies"
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- "ci"
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commit-message:
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prefix: "chore(ci)"
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include: "scope"

‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches: [main, develop]
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pull_request:
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branches: [main, develop]
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workflow_dispatch:
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jobs:
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lint:
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name: Lint and Type Check
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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cache: 'pip'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements-dev.txt
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- name: Run flake8
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run: |
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flake8 cli_audit tests --count --select=E9,F63,F7,F82 --show-source --statistics
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flake8 cli_audit tests --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Run mypy
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run: |
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mypy cli_audit --ignore-missing-imports
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continue-on-error: true
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test:
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name: Test Suite
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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python-version: ['3.9', '3.10', '3.11', '3.12']
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements-dev.txt
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- name: Run unit tests
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run: |
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pytest tests/unit -v --cov=cli_audit --cov-report=xml --cov-report=term
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- name: Run integration tests
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run: |
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pytest tests/integration -v --cov=cli_audit --cov-append --cov-report=xml --cov-report=term
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v4
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with:
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file: ./coverage.xml
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flags: unittests
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name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
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fail_ci_if_error: false
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security:
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name: Security Scan
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install bandit safety
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- name: Run bandit
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run: |
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bandit -r cli_audit -f json -o bandit-report.json || true
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bandit -r cli_audit
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continue-on-error: true
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- name: Run safety check
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run: |
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safety check --json || true
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safety check
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continue-on-error: true
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build:
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name: Build Distribution
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runs-on: ubuntu-latest
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needs: [lint, test]
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install build tools
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run: |
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python -m pip install --upgrade pip
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pip install build twine
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- name: Build package
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run: |
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python -m build
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- name: Check package
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run: |
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twine check dist/*
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- name: Upload artifacts
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uses: actions/upload-artifact@v4
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with:
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name: distributions
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path: dist/
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docs:
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name: Documentation Check
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Check README
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run: |
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python -m pip install --upgrade pip
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pip install markdown
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python -c "import markdown; markdown.markdown(open('README.md').read())"
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- name: Validate YAML configs
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run: |
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pip install pyyaml
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python -c "import yaml; yaml.safe_load(open('.cli-audit.yml').read())" || echo "No config file"
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integration-e2e:
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name: End-to-End Integration
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runs-on: ubuntu-latest
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needs: [test]
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install package
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run: |
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python -m pip install --upgrade pip
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pip install -e .
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- name: Test CLI execution
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run: |
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python cli_audit.py --help
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CLI_AUDIT_JSON=1 python cli_audit.py --only python-core | jq '.'
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- name: Test programmatic API
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run: |
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python -c "from cli_audit import Config, Environment, load_config; c = Config(); print('✓ API works')"

‎.github/workflows/release.yml‎

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name: Release
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on:
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push:
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tags:
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- 'v*.*.*'
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workflow_dispatch:
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permissions:
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contents: write
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jobs:
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build:
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name: Build Distribution
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install build tools
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run: |
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python -m pip install --upgrade pip
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pip install build twine
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- name: Build package
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run: |
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python -m build
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- name: Check package
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run: |
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twine check dist/*
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- name: Upload artifacts
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uses: actions/upload-artifact@v4
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with:
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name: distributions
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path: dist/
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release:
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name: Create GitHub Release
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runs-on: ubuntu-latest
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needs: [build]
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Download artifacts
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uses: actions/download-artifact@v4
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with:
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name: distributions
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path: dist/
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- name: Extract version
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id: version
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run: |
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echo "VERSION=${GITHUB_REF#refs/tags/v}" >> $GITHUB_OUTPUT
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- name: Generate changelog
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id: changelog
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run: |
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# Extract changes for this version from CHANGELOG if it exists
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if [ -f CHANGELOG.md ]; then
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echo "CHANGES<<EOF" >> $GITHUB_OUTPUT
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sed -n "/^## \[${VERSION}\]/,/^## \[/p" CHANGELOG.md | sed '$d' >> $GITHUB_OUTPUT || echo "See CHANGELOG.md for details" >> $GITHUB_OUTPUT
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echo "EOF" >> $GITHUB_OUTPUT
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else
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echo "CHANGES=Release ${{ steps.version.outputs.VERSION }}" >> $GITHUB_OUTPUT
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fi
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env:
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VERSION: ${{ steps.version.outputs.VERSION }}
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- name: Create Release
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uses: softprops/action-gh-release@v1
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with:
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files: dist/*
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body: ${{ steps.changelog.outputs.CHANGES }}
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draft: false
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prerelease: ${{ contains(github.ref, 'alpha') || contains(github.ref, 'beta') || contains(github.ref, 'rc') }}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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publish-pypi:
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name: Publish to PyPI
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runs-on: ubuntu-latest
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needs: [build, release]
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
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steps:
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- name: Download artifacts
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uses: actions/download-artifact@v4
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with:
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name: distributions
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path: dist/
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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password: ${{ secrets.PYPI_API_TOKEN }}
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skip-existing: true
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publish-test-pypi:
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name: Publish to Test PyPI
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runs-on: ubuntu-latest
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needs: [build]
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if: github.event_name == 'workflow_dispatch'
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steps:
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- name: Download artifacts
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uses: actions/download-artifact@v4
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with:
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name: distributions
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path: dist/
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- name: Publish to Test PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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password: ${{ secrets.TEST_PYPI_API_TOKEN }}
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repository-url: https://test.pypi.org/legacy/
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skip-existing: true

‎.gitignore‎

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# Node.js (minimal usage for Claude Code dependency)
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node_modules/
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# AI agent session context (not committed)
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claudedocs/

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