I can't reproduce this issue. Here's what I've done:

- Installed Hardy
- Disabled -updates and -security in /etc/apt/sources.list
- sudo apt-get install mysql-server-5.0
- Directory /etc/mysql/conf.d exists with old_passwords.cnf in it
- Enabled -updates and -security in /etc/apt/sources.list
- sudo apt-get dist-upgrade
- Directory /etc/mysql/conf.d still exists (with no files in it)
- Mysql starts fine

Also, I took a look at all the scripts in the mysql package, and I don't
see where any of them could remove that directory.

I am not sure why you're getting this issue. Is there anything else you
are installing or doing to reproduce it?

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mysql refuses to start after security update
https://bugs.launchpad.net/bugs/305107
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