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Because you have on line 59 variable $migrationFileName without .php and you set it:
so you must check existing migrations (function migrationFileExists) with .php extension too.
If you don't do that, condition can not work properly, e.g. current functionality return false te_users_table.php === create_users_table.
This pull request fix this condition and it will return true _create_users_table.php === create_users_table.php.