This is due to mysql-common package installed via apt. You do no need to remove it if there is a depency, instead issue the following commands:
rm /etc/mysql/my.cnf
ln -s /etc/my.cnf /etc/mysql/my.cnf
/etc/init.d/mysqld start
ps ax | grep sql
Output should be like:
# ps ax | grep sql
13126 ? S 0:00 /bin/sh /usr/local/mysql/bin/mysqld_safe --user=mysql --datadir=/usr/local/mysql/data --pid-file=/usr/local/mysql/data/diver.pid
13185 ? Sl 5:19 /usr/local/mysql/bin/mysqld --basedir=/usr/local/mysql --datadir=/usr/local/mysql/data --user=mysql --log-error=/usr/local/mysql/data/diver.guru-host.eu.err --pid-file=/usr/local/mysql/data/diver.pid
14982 pts/0 R+ 0:00 grep sql
