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I took care about bug against "mysql_secure_installation" script. 
The problem is pretty simple.
When you use "mysql_secure_installation" script, it will ingore all of
yours current configuration.
However, there are some options, that can be used. One of them is used to
add your custom config file. It is documented, for example, here: 
Unfortunatelly, the "man mysql_secure_installation" is quite short of
infromation. (same as )
I believe, the information about options really should be added to both
manpage and .
That should also solve the bug, without any
I would like your general opinion about this.
Based on it, I can file issue on JIRA.
Core Services - Databases Team