Load AppConfig at runtime and wire logging into CLI & API

[aidankhogg]

Motivation

• Provide a single runtime configuration entrypoint so process-level settings (especially logging) can be declared in an AppConfig file or via NETENGINE_CONFIG rather than scattered env/defaults.
• Ensure FastAPI and CLI startup paths initialize logging from the same structured config so logs are consistent across entrypoints.
• Keep spec files focused on world topology while making runtime concerns declarative and easier to test.

Description

• Added netengine/config/runtime.py with helpers: load_app_config, configure_logging, and load_runtime_config that use ConfigLoader.load_config(AppConfig, ...) and map AppConfig.logging to the existing LoggerFactory via a generated RuntimeLogConfig class.
• Wired runtime loading into the CLI group by adding a --config option (envvar NETENGINE_CONFIG) which calls load_runtime_config(config_file) during CLI startup.
• Invoked load_runtime_config() at FastAPI import time in netengine/api/app.py so the API process applies the same logging defaults.
• Added tests in tests/test_config.py to verify a minimal runtime config file applies logging defaults and that the CLI --config option passes runtime logging settings to the logger factory.

Testing

• Ran linter: python -m ruff check netengine/config/runtime.py netengine/api/app.py netengine/cli/main.py tests/test_config.py and it passed.
• Ran targeted pytest: pytest -q tests/test_config.py tests/test_cli.py::test_poetry_console_script_points_to_click_group and the tests passed.
• Ran the CLI test suite: pytest -q tests/test_cli.py and all tests passed; full test run showed 47 passed for the combined runs including the new tests.

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Codex Task