Думаю, имеет смысл по умолчанию добавить в my.cnf опцию: [mysqld] innodb_file_per_table Обоснование видно, например, отсюда: http://stackoverflow.com/questions/3456159/how-to-shrink-purge-ibdata1-file-in-mysql
На Sisyphus
MySQL-5.5.28-alt2 -> sisyphus: * Thu Oct 11 2012 Michael Shigorin <mike@altlinux> 5.5.28-alt2 - fixed one-byte postun trigger thinko (included current version) * Thu Oct 11 2012 Michael Shigorin <mike@altlinux> 5.5.28-alt1 - 5.5.28 (closes: #27016) + NB: innodb is builtin *again*, please pay attention to my.cnf - use innodb_file_per_table (closes: #27072) - fixed charset handling in initscript (closes: #26817) - implemented extendedstatus in initscript (closes: #7719) - implemented basic control facility (lnkvisitor@) * Mon Jun 18 2012 Dmitriy Kulik <lnkvisitor@altlinux> 5.5.25-alt1 - Test build Mysql 5.5.25
