In main.m change addPersistentStoreWithType:… options: from nil to @{NSSQLitePragmasOption:@{ @"journal_mode" : @"DELETE" }}. Now run program to generate 1 sqlite file instead of 3.

Reference:
http://www.raywenderlich.com/12170/core-data-tutorial-how-to-preloadimport-existing-data-updated
Comment by leuco on 2013-11-09