test: cover project config precedence

[haosenwang1018]

Summary

• add direct coverage proving project TOML overrides global TOML during config resolution
• verify set_config_value(..., project=True) writes to PROJECT_CONFIG_PATH instead of the global config file
• keep the change focused on real config precedence behavior shared by multiple CLI entrypoints

Testing

• uv run ruff format tests/test_config.py
• uv run ruff check tests/test_config.py
• uv run python -m pytest tests/test_config.py -q

Closes #114

[zc277584121]

Closing — the project config precedence tests are covered more comprehensively in #280. Thanks!