Comment 1 for bug 1370522

From the docs: http://www.percona.com/doc/percona-xtrabackup/2.2/xtrabackup-files.html

- backup-my.cnf

This file contains information to start the mini instance of InnoDB during the --apply-log. This is NOT a backup of original my.cnf. The InnoDB configuration is read from the file backup-my.cnf created by innobackupex when the backup was made. innobackupex --apply-log uses InnoDB configuration from backup-my.cnf by default, or from innobackupex --defaults-file, if specified. InnoDB configuration in this context means server variables that affect data format, i.e. innodb_page_size, innodb_log_block_size, etc. Location-related variables, like innodb_log_group_home_dir or innodb_data_file_path are always ignored by innobackupex --apply-log, so preparing a backup always works with data files from the backup directory, rather than any external ones.