MySQL not picking up symlinked cnf changes in 5.7.13 on Ubuntu 16.04 - mysql

Question

EDIT: I may have found what might be part of the issue, further edit at the bottom.
I've got a new server setup running mysql everything seems to be okay. Except whenever I use show variables the configuration settings I can see in my .cnf file are not being shown and what appear to be general defaults are being shown. So it would appear while I can use mysql just fine, the settings are all just the defaults.
I am trying to figure out why my .cnf is not being used. I have taken a number of steps to check that it is definitely being loaded and these are laid out below. Once I am sure it is being loaded I am at a loss as to how to explain why my settings aren't being used. Any help would be greatly appreciated.
The location of my cnf file is this:
/etc/mysql/mysql.conf.d/mysqld.cnf
I have attempted to verify that this is what is being used by the following:
sudo /usr/sbin/mysqld --verbose --help | grep -A 1 "Default options"
Default options are read from the following files in the given order:
/etc/my.cnf /etc/mysql/my.cnf ~/.my.cnf
/etc/my.cnf does not exist
/etc/mysql/my.cnf is a symlink to /etc/alternatives/my.cnf
/etc/alternatives/my.cnf is a symlink to /etc/mysql/mysql.cnf
/etc/mysql/mysql.cnf contains:
!includedir /etc/mysql/conf.d/
!includedir /etc/mysql/mysql.conf.d/
etc/mysql/conf.d/ is a directory that contains:
mysql.cnf
mysqldump.cnf
mysql.cnf is empty so presumably isn’t doing anything
/etc/mysql/mysql.conf.d/ is a directory that contains:
mysqld.cnf
mysqld.cnf.dpkg-new
mysqld_safe_syslog.cnf
mysqld.cnf is a symlink to /home/{my_username}/conf/mysqld.cnf
/home/{my_username}/conf/mysqld.cnf is my conf file which I expect it to be using.
So I cannot see the problem it looks like it should be using my config.
In a second attempt to verify that this .cnf is being used I used strace mysql. My file was listed and opened along with the other paths I just listed above.
stat("/etc/mysql/mysql.conf.d/mysqld.cnf", {st_mode=S_IFREG|0664, st_size=2262, ...}) = 0
open("/etc/mysql/mysql.conf.d/mysqld.cnf", O_RDONLY) = 4
fstat(4, {st_mode=S_IFREG|0664, st_size=2262, ...}) = 0
read(4, "# Generated by Percona Configura"..., 4096) = 2262
read(4, "", 4096) = 0
close(4) = 0 close(4)
Again it looks like it should be using the .cnf file.
Can anyone offer any insight into why it's not?
EDIT: I've just done a strace mysqld instead of strace mysql and I get a permission error on my .cnf file. This could be the problem. But I don't understand enough about the difference between mysql and mysqld can anyone explain?
stat("/etc/mysql/mysql.conf.d/mysqld.cnf", {st_mode=S_IFREG|0664, st_size=3218, ...}) = 0
open("/etc/mysql/mysql.conf.d/mysqld.cnf", O_RDONLY) = -1 EACCES (Permission denied)

Answer 1

This was caused and resolved by apparmor
Ubuntu comes with something called AppArmor, a kernel-integrated
application security system that controls how applications can access
the file system. Source: Oracle Article
If you put the .cnf in a custom location, you need to give mysql permissions to access that directory. In my case I needed to edit this /etc/apparmor.d/local/usr.sbin.mysqld with the following:
/home/{my_username}/conf/mysqld.cnf r
You could also use:
/home/{my_username}/conf/* r
To give it access to the whole directory.