feat: implement comprehensive code quality tools and enforcement

Author: jzhu

.flake8

@@ -0,0 +1,37 @@
+[flake8]
+# Flake8 configuration for code-assistant-manager
+
+# Compatibility with Black
+max-line-length = 88
+extend-ignore = E203, W503, E501
+
+# Exclude patterns
+exclude =
+    .git,
+    __pycache__,
+    .venv,
+    venv,
+    env,
+    .eggs,
+    *.egg,
+    build,
+    dist,
+    .tox,
+    .mypy_cache,
+    .pytest_cache,
+    node_modules,
+    *.egg-info
+
+# Complexity
+max-complexity = 15
+
+# McCabe complexity
+# Default is 10, we allow slightly more for complex CLI logic
+per-file-ignores =
+    __init__.py:F401,F403
+    cli.py:C901
+    tools/base.py:C901
+
+# Plugins configuration
+# flake8-bugbear, flake8-comprehensions, flake8-simplify
+select = C,E,F,W,B,B9

.pre-commit-config.yaml

@@ -1,25 +1,77 @@
 repos:
+  # Standard pre-commit hooks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
+        exclude: '\.patch$'
       - id: end-of-file-fixer
+        exclude: '\.patch$'
       - id: check-yaml
+      - id: check-json
       - id: check-added-large-files
+        args: ['--maxkb=1000']
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: debug-statements
+      - id: mixed-line-ending
+        args: ['--fix=lf']
 
+  # Python code formatting
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 24.3.0
     hooks:
       - id: black
+        language_version: python3
+        args: ['--config=pyproject.toml']
 
+  # Import sorting
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ['--profile=black', '--line-length=88']
+
+  # Linting
   - repo: https://github.com/pycqa/flake8
     rev: 7.1.2
     hooks:
       - id: flake8
-        args: [--max-line-length=88, --extend-ignore=E203,W503]
+        args: ['--config=.flake8']
+        additional_dependencies: [
+          'flake8-bugbear',
+          'flake8-comprehensions',
+          'flake8-simplify',
+        ]
 
+  # Type checking
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.11.0
     hooks:
       - id: mypy
-        additional_dependencies: [types-PyYAML]
+        args: ['--config-file=pyproject.toml']
+        additional_dependencies: [
+          'types-PyYAML',
+          'types-requests',
+          'pydantic>=2.6.0',
+          'typer>=0.12.0',
+        ]
+        exclude: '^tests/'
+
+  # Security checks
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.7.8
+    hooks:
+      - id: bandit
+        args: ['-c', 'pyproject.toml']
+        additional_dependencies: ['bandit[toml]']
+        exclude: '^tests/'
+
+  # Docstring coverage
+  - repo: https://github.com/econchick/interrogate
+    rev: 1.7.0
+    hooks:
+      - id: interrogate
+        args: ['--config=pyproject.toml']
+        pass_filenames: false

CLAUDE.md

@@ -2,13 +2,105 @@
 
 This file documents repository-level expectations and instructions intended to guide contributors and AI-assisted editing tools (like Claude Code) when making changes in this project.
 
-- Ask for approval before any git commit and push
-- Always run tests before completing all development of new changes
-- Always test the CLI usages
-- After any changes, run the folling to reinstall the project:
-```
+## Core Guidelines
+
+- **Ask for approval before any git commit and push**
+- **Always run tests** before completing all development of new changes
+- **Always test the CLI usages** to ensure functionality works end-to-end
+- **Run code quality checks** before committing (see below)
+
+## Development Workflow
+
+### After Any Changes
+
+Reinstall the project to test in production-like environment:
+
+```bash
 rm -rf dist/*
 ./install.sh uninstall
 ./install.sh
 cp ~/.config/code-assistant-manager/settings.json.bak ~/.config/code-assistant-manager/settings.json
 ```
+
+### Code Quality Requirements
+
+Before committing, ensure all quality checks pass:
+
+```bash
+# Quick check (formatting + linting + type-check + tests)
+make check
+
+# Or run individually:
+make format          # Auto-format code with Black and isort
+make lint            # Check code style with Flake8
+make type-check      # Verify type hints with mypy
+make security        # Scan for security issues with Bandit
+make test            # Run test suite
+```
+
+**Pre-commit hooks** are automatically installed with `make dev-install` and will run these checks before each commit.
+
+### Code Style Standards
+
+- **Formatting**: Use Black (line length: 88)
+- **Import sorting**: Use isort (Black-compatible profile)
+- **Linting**: Follow Flake8 rules (see `.flake8`)
+- **Type hints**: Add type hints for new code (checked with mypy)
+- **Docstrings**: Use Google-style docstrings for public functions/classes
+- **Security**: No hardcoded secrets, follow Bandit recommendations
+
+### Testing Requirements
+
+- Write tests for all new functionality
+- Maintain or improve test coverage
+- Use appropriate test markers (`@pytest.mark.unit`, `@pytest.mark.integration`, etc.)
+- Mock external dependencies (APIs, file system, network)
+
+## Quick Reference
+
+### Setup Development Environment
+
+```bash
+# One-time setup
+make dev-install     # Install with dev dependencies + pre-commit hooks
+```
+
+### Common Commands
+
+```bash
+make help            # Show all available commands
+make format          # Auto-format code
+make check           # Run all quality checks
+make test            # Run test suite
+make test-cov        # Run tests with coverage report
+```
+
+### Before Submitting Code
+
+1. ✅ Run `make check` - All checks must pass
+2. ✅ Run `make test` - All tests must pass
+3. ✅ Test CLI manually - Ensure functionality works
+4. ✅ Update documentation - If adding/changing features
+5. ✅ Review changes - Use `git diff` before committing
+
+## Documentation
+
+- See `CONTRIBUTING.md` for detailed contribution guidelines
+- See `docs/CODE_QUALITY.md` for comprehensive code quality tool documentation
+- See `docs/DESIGN_PATTERNS_README.md` for architecture patterns
+
+## Attribution
+
+When using AI assistance for code generation, add attribution in commit messages:
+
+```bash
+git commit -m "feat: implement new feature
+
+Co-Authored-By: Claude <noreply@anthropic.com>"
+```
+
+## Questions?
+
+- Review this document and `CONTRIBUTING.md`
+- Check code quality documentation in `docs/CODE_QUALITY.md`
+- Consult design patterns guide in `docs/DESIGN_PATTERNS_README.md`