This is a bug in MySQL. When the embedded MySQL server starts, it fails 
to read ~/.kde4/share/apps/amarok/my.cnf, therefore does not set a local 
datadir and tries to create the Amarok database in /var/db/mysql, the 
built-in default.

The only work-around I am aware of (and that I am using myself) is to 
copy ~/.kde4/share/apps/amarok/my.cnf to /usr/local/etc/my.cnf. 
Obviously, this is an awful hack as it redirects MySQL databases into 
your Amarok directory system-wide. But yours is a desktop system, maybe 
you can live with that.

- Bartosz
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