Fix bool conversion in config

[luispedro]

Summary

• fix read_configuration_file to handle booleans correctly
• add test verifying boolean options read from config files

Testing

• pytest jug/tests/test_options.py::test_bool_from_config -q
• pytest -q (fails: PermissionError not raised in test_file_store)

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https://chatgpt.com/codex/tasks/task_e_68706f74a7708333a636882e32c08f08