Resolve config-relative paths from the config file directory

[biefan]

Summary

• resolve relative initialization_scripts and env_files from the configuration file directory when loading YAML config files
• preserve the existing current-working-directory behavior for CLI path overrides
• add regression tests for both from_yaml_file() and load_with_overrides(config_file=...)

Problem

ConfigurationLoader currently resolves relative initialization_scripts and env_files from the caller's working directory. When a config file lives in another directory, values like ./scripts/init.py or ./env/local.env point to the wrong files.

Validation

• .venv/bin/pytest tests/unit/setup -q
• .venv/bin/ruff check pyrit/setup/configuration_loader.py tests/unit/setup/test_configuration_loader.py