generate_config_file: Writing empty sets

IMHO; empty sets should be written as `set([])` (not `set()`), since when you later add some values, it is easy to forget adding the `[]`. Yes, you can also use set literals, but then the existing `set()` does not nudge you into that direction.

Start at the generate_config_file entry point and inspect how empty sets are serialized. The change is complete when an empty set is emitted as set([]) rather than set(), with the existing test coverage run to confirm the generated configuration remains valid.

Written by the indexing model from the issue text.