What options in /etc/mysql/my.cnf are applicable to percona-server-client-5.6?
Those other sections are there because they are included in the template cnf file from the package provider (Percona).

You can create a user specific cnf file in your home dir that looks like the one below and they will get used when you run the mysql command:

[client]
user=$myusername
password=$mypassword


n.b. if you're going to store your credentials in a cnf file make sure you  set the permissions to 400.