As far as I know there isn't a well accepted set of best practices for MySQL, but there are many best practices known and used by most MySQL DBA's. One of those best practices is that the datadir must not be equal to a mountpoint; it has to be a subdirectory of a mountpoint. I learned this the hard way a few years ago when I used a NetApp Filer via NFS as a data directory. The NetApp filer exposed the snapshots via a .snapshot directory. A database in MySQL is a directory, so MySQL thought that the .snapshot directory was a database. This resulted in some issues with our monitoring scripts, so we had to create a mysql_data directory and move all the databases to that directory. For other setups directories like lost+found, .zfs, etc. gave similar issues. In MySQL 5.6 a new feature was introduced to make it possible to make some databases hidden. To do this a ignore-db-dir option needs to be specified for each directory. On a running server the list of ignored database direc...