I initially asked about this on the mariadb-discuss list:

https://lists.launchpad.net/maria-discuss/msg01912.html

I've also submitted this as bug 74551 to Oracle:

http://bugs.mysql.com/bug.php?id=74551

If an includedir directive like the following is added to /etc/my.cnf:

!includedir /home/mysql/conf

MySQL should load any configuration variables from files in that directory if the file name ends with '.cnf' according to the documentation:

http://dev.mysql.com/doc/refman/5.6/en/option-files.html

The problem I ran into is that MySQL appears to do the comparison based on the first dot character ('.') that appears in the filename. If I have a file with a full path like this:

/home/mysql/conf/mysql5.6.cnf

MySQL appears to think that the extension of the file is '.6.cnf', rather than '.cnf', so it won't load configuration variables from it.

How to repeat:
Add an includedir directive to my.cnf.

In the directory named in the includedir directive, add a file with a name that adds in .cnf, but also has at least one additional dot character ('.') in the name.

Suggested fix:
Perform the comparison by seeing that the file name ends with '.cnf', rather than comparing against the string that appears after the first dot character ('.').