fix: At the end of tuning script, the resulting config file does not retain comments from the original config file.

[LucasDedieu]

Description

At the end of tuning script, the resulting config file does not retain comments from the original config file.

How to reproduce the bug

1. Launch a tuning process using a config file that contains comments.
2. At the end of tuning, the resulting config file in output_dir has lost all comments.