It does in fact appear to be an apparmor problem, the kern.log has multiple
May 18 08:51:39 orac kernel: [79075.568386] audit: type=1400 audit(1431953499.358:167): apparmor="DENIED" operation="open" profile="/usr/sbin/mysqld" name="/etc/mysql/mysql.conf.d/" pid=7960 comm="mysqld" requested_mask="r" denied_mask="r" fsuid=122 ouid=0
It does in fact appear to be an apparmor problem, the kern.log has multiple
May 18 08:51:39 orac kernel: [79075.568386] audit: type=1400 audit(143195349 9.358:167) : apparmor="DENIED" operation="open" profile= "/usr/sbin/ mysqld" name="/ etc/mysql/ mysql.conf. d/" pid=7960 comm="mysqld" requested_mask="r" denied_mask="r" fsuid=122 ouid=0