refactor: replace run_tests.py with makefile for pytest best practices

- Replace custom test runner with standard Makefile approach
- Add comprehensive test targets (unit, integration, security, config)
- Include quality checks (mypy, ruff) after successful tests
- Restore ThoughtProcessor implementation into server_core.py
- Fix integration tests to use proper mocking patterns
- Update documentation in CLAUDE.md and READMEs
- Add .gitignore rules for temporary test files

All 69 tests passing. Follows pytest best practices with direct
pytest execution through make targets instead of wrapper scripts.

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

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

Author: FradSer

.gitignore

@@ -17,3 +17,7 @@ wheels/
 htmlcov/
 .coverage.*
 test-results.xml
+
+# Temporary test files in root (avoid creating these)
+/test_*.py
+/TEST_*.md

CLAUDE.md

@@ -8,10 +8,18 @@ uv pip install -e ".[dev]"                              # Install dependencies
 uv run mcp-server-mas-sequential-thinking               # Run server
 uv run ruff check . --fix && uv run ruff format . && uv run mypy .  # Code quality
 
-# Testing Framework
-python run_tests.py                                     # Run all tests with coverage
-python run_tests.py --unit --security                   # Run unit and security tests
-uv run pytest tests/ -v                                 # Direct pytest execution
+# Testing Framework (using Makefile)
+make test                                               # Run all tests with coverage + quality checks
+make test-unit                                          # Run unit tests only
+make test-fast                                          # Fast run without coverage
+make test-parallel                                      # Run tests in parallel
+make test-coverage                                      # Generate HTML coverage report
+make help                                               # Show all available commands
+
+# Direct Pytest Commands
+uv run pytest tests/ -v                                 # Run all tests
+uv run pytest -m unit                                   # Run tests with specific marker
+uv run pytest --no-cov                                  # Skip coverage
 
 # Debugging & Monitoring
 tail -f ~/.sequential_thinking/logs/sequential_thinking.log          # Live logs

Makefile

@@ -0,0 +1,127 @@
+# Makefile for MCP Sequential Thinking Server
+# Provides convenient commands for testing and development
+
+.PHONY: help test test-unit test-integration test-security test-config test-fast test-debug test-quiet test-parallel test-coverage test-junit check-types lint check-all clean
+
+# Default target: show help
+help:
+	@echo "MCP Sequential Thinking Server - Test Commands"
+	@echo ""
+	@echo "Test Execution:"
+	@echo "  make test              - Run all tests with coverage (default)"
+	@echo "  make test-unit         - Run only unit tests"
+	@echo "  make test-integration  - Run only integration tests"
+	@echo "  make test-security     - Run only security tests"
+	@echo "  make test-config       - Run only configuration tests"
+	@echo "  make test-fast         - Run tests without coverage (faster)"
+	@echo "  make test-debug        - Run tests in debug mode (verbose)"
+	@echo "  make test-quiet        - Run tests with minimal output"
+	@echo "  make test-parallel     - Run tests in parallel"
+	@echo ""
+	@echo "Coverage & Reports:"
+	@echo "  make test-coverage     - Run tests with HTML coverage report"
+	@echo "  make test-junit        - Run tests with JUnit XML report"
+	@echo ""
+	@echo "Code Quality:"
+	@echo "  make check-types       - Run mypy type checking"
+	@echo "  make lint              - Run ruff linting"
+	@echo "  make check-all         - Run all quality checks (tests + types + lint)"
+	@echo ""
+	@echo "Cleanup:"
+	@echo "  make clean             - Remove test artifacts and cache files"
+
+# Run all tests with coverage (default behavior)
+test:
+	@echo "Running all tests with coverage..."
+	@uv run pytest tests/ --cov=src/mcp_server_mas_sequential_thinking --cov-report=term-missing -v --tb=short
+	@$(MAKE) -s check-types
+	@$(MAKE) -s lint
+
+# Run only unit tests
+test-unit:
+	@echo "Running unit tests..."
+	@uv run pytest tests/unit/ --cov=src/mcp_server_mas_sequential_thinking --cov-report=term-missing -v --tb=short
+	@$(MAKE) -s check-types
+	@$(MAKE) -s lint
+
+# Run only integration tests
+test-integration:
+	@echo "Running integration tests..."
+	@uv run pytest tests/integration/ --cov=src/mcp_server_mas_sequential_thinking --cov-report=term-missing -v --tb=short
+	@$(MAKE) -s check-types
+	@$(MAKE) -s lint
+
+# Run only security tests (using markers)
+test-security:
+	@echo "Running security tests..."
+	@uv run pytest -m security --cov=src/mcp_server_mas_sequential_thinking --cov-report=term-missing -v --tb=short
+	@$(MAKE) -s check-types
+	@$(MAKE) -s lint
+
+# Run only configuration tests (using markers)
+test-config:
+	@echo "Running configuration tests..."
+	@uv run pytest -m config --cov=src/mcp_server_mas_sequential_thinking --cov-report=term-missing -v --tb=short
+	@$(MAKE) -s check-types
+	@$(MAKE) -s lint
+
+# Run tests without coverage (faster)
+test-fast:
+	@echo "Running tests without coverage (fast mode)..."
+	@uv run pytest tests/ -v --tb=short --no-cov
+
+# Run tests in debug mode (verbose, no capture, long tracebacks)
+test-debug:
+	@echo "Running tests in debug mode..."
+	@uv run pytest tests/ -vv -s --tb=long --no-cov
+
+# Run tests with minimal output
+test-quiet:
+	@echo "Running tests (quiet mode)..."
+	@uv run pytest tests/ -q --tb=short --no-cov
+
+# Run tests in parallel
+test-parallel:
+	@echo "Running tests in parallel..."
+	@uv run pytest tests/ --cov=src/mcp_server_mas_sequential_thinking --cov-report=term-missing -v --tb=short -n auto
+	@$(MAKE) -s check-types
+	@$(MAKE) -s lint
+
+# Run tests with HTML coverage report
+test-coverage:
+	@echo "Running tests with HTML coverage report..."
+	@uv run pytest tests/ --cov=src/mcp_server_mas_sequential_thinking --cov-report=term-missing --cov-report=html -v --tb=short
+	@echo "Coverage report generated in htmlcov/index.html"
+	@$(MAKE) -s check-types
+	@$(MAKE) -s lint
+
+# Run tests with JUnit XML report
+test-junit:
+	@echo "Running tests with JUnit XML report..."
+	@uv run pytest tests/ --cov=src/mcp_server_mas_sequential_thinking --cov-report=term-missing -v --tb=short --junit-xml=test-results.xml
+	@echo "JUnit report generated: test-results.xml"
+	@$(MAKE) -s check-types
+	@$(MAKE) -s lint
+
+# Run mypy type checking
+check-types:
+	@echo "Type checking with mypy..."
+	@uv run mypy src --ignore-missing-imports
+
+# Run ruff linting
+lint:
+	@echo "Linting with ruff..."
+	@uv run ruff check src tests
+
+# Run all quality checks (tests, type checking, linting)
+check-all: test check-types lint
+	@echo "All quality checks passed!"
+
+# Clean up test artifacts and cache files
+clean:
+	@echo "Cleaning test artifacts and cache files..."
+	@rm -rf .pytest_cache .coverage htmlcov test-results.xml
+	@find . -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null || true
+	@find . -type d -name ".mypy_cache" -exec rm -rf {} + 2>/dev/null || true
+	@find . -type d -name ".ruff_cache" -exec rm -rf {} + 2>/dev/null || true
+	@echo "Clean complete!"

README.md

@@ -461,7 +461,7 @@ mcp-server-mas-sequential-thinking/
 │   │   ├── ai_complexity_analyzer.py    # AI-powered analysis
 │   │   └── multi_thinking_router.py     # Intelligent routing
 │   ├── services/
-│   │   ├── thought_processor_refactored.py
+│   │   ├── server_core.py                   # ThoughtProcessor implementation
 │   │   ├── workflow_executor.py
 │   │   └── context_builder.py
 │   └── config/

README.zh-CN.md

@@ -461,7 +461,7 @@ mcp-server-mas-sequential-thinking/
 │   │   ├── ai_complexity_analyzer.py    # AI 驱动分析
 │   │   └── multi_thinking_router.py     # 智能路由
 │   ├── services/
-│   │   ├── thought_processor_refactored.py
+│   │   ├── server_core.py                   # ThoughtProcessor 实现
 │   │   ├── workflow_executor.py
 │   │   └── context_builder.py
 │   └── config/