"As of MySQL 5.6.8, on Unix platforms, mysql_install_db creates a default option file named my.cnf in the base installation directory. This file is created from a template included in the distribution package named my-default.cnf. You can find the template in or under the base installation directory."
So, if basedir is /usr and mysql_install_db is called in the process, this looks like an expected and documented (even if new and unexpected) upstream MySQL 5.6 behavior.
Why do we think this is a bug? Looks like /usr/my.cnf is a new and documented "feature" of upstream MySQL 5.6. Check:
http:// dev.mysql. com/doc/ refman/ 5.6/en/ mysql-install- db.html:
"As of MySQL 5.6.8, on Unix platforms, mysql_install_db creates a default option file named my.cnf in the base installation directory. This file is created from a template included in the distribution package named my-default.cnf. You can find the template in or under the base installation directory."
http:// bugs.mysql. com/bug. php?id= 68318 bugs.mysql. com/bug. php?id= 68416
http://
...
So, if basedir is /usr and mysql_install_db is called in the process, this looks like an expected and documented (even if new and unexpected) upstream MySQL 5.6 behavior.