pt-config-diff doesn't respect !includedir
pt-config-diff from percona toolkit 2.1.2, used to compare a running MySQL instance with its installed config files on the filesystem, doesn't properly represent the state of the config files if !includedir or !include is used (as is common on Debian and Ubuntu).
pt-config-diff /etc/mysql/my.cnf u=root,
The comparison is made only between my.cnf and MySQL's running config, which is not really as expected.
It can be worked around with something like the following:
cat $(find /etc/mysql/ -type f -regex .*cnf -printf %p\ ) > /tmp/mysql.cnf
and then using the output file with pt-config-diff.