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MySQL InnoDB File Per Table

By default MySQL 5.5 and prior store all InnoDB tables in a single table space or file. Improved performance and managability can be accheived by using the innodb_file_per_table option to cause MySQL to use a separate file for each table. This option is enabled by default on MySQL 5.6 and later.

To implement:
1. Add option to my.cnf:

2. Change table to use single file:

If you want to covert all databases then dump the entire database and import back into the server.