innodb_file_per_table is by default ON Mysql 5.6.6 and onwards. There is plenty of stuff on Google about pros & cons ofinnodb_file_per_table.
This post details how to enable innodb_file_per_table on an existing database. Because innodb_file_per_table affects new tables only, created after innodb_file_per_table is enabled, we need to recreate old databases to force innodb_file_per_table on old tables and reclaim some disk space.
Backup First
Create a dir to take backups:
cd ~ mkdir backup cd backup