[phpMyAdmin Developers] Problem in setup script

[Raghuram Vadapalli]

Hi everyone,

I am working on improving setup script [1]. I encountered a few bugs after
starting to work on it. I fixed a few of them. Now I am facing another
issue. After modifying/setting values and applaying them. The setup doesn't
retain those options. It shows basic configuration file when I try to
display them using display option. It will be great if someone can help me
fix it. You can checkout my branch from Github [2].

[1] https://github.com/phpmyadmin/phpmyadmin/issues/12844
[2] https://github.com/Achilles-96/phpmyadmin/tree/Setup-Improvements

Regards,
Raghuram
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