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

[romanlutz]

Thanks for identifying the real bug. Relative paths resolving from cwd instead of the config file directory is worth fixing. However, this can be solved much more simply by eagerly resolving relative paths to absolute at YAML load time (in from_yaml_file), which avoids the new hidden state fields and plumbing through load_with_overrides. The initializer construction change should also be a separate PR.

I'm submitting a separate PR #1650 since it's a significant amount of change from this PR.