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The instance manager was not actually checking whether an instance was actually running before trying to stop it. Now it checks first.
Instance Manager - manage MySQL instances locally and remotely. File description: mysqlmanager.cc - entry point to the manager, main, options.{h,cc} - handle startup options manager.{h,cc} - manager process mysql_connection.{h,cc} - handle one connection with mysql client. See also instance manager architecture description in mysqlmanager.cc.