Close all output and log files explicitly

[boolean5]

Currently, main() explicitly closes only the output and log file pair that corresponds to the last configuration section. This happens because close is called outside of the for loop that processes the configuration sections.

The rest of the files are most probably closed automatically because of CPython's reference counting. However, we should not rely on this, as it is an implementation detail specific to CPython and not a language feature.

I suggest moving the calls to close inside the for loop.

get_versioned_lists seems to be doing the same thing.