Array
(
    [database] => Array
        (
            [0] => CREATE  TABLE IF NOT EXISTS `test` (
                  `testid` VARCHAR(255) NOT NULL ,
                  `name` VARCHAR(45) NOT NULL ,
                  `type` VARCHAR(45) NOT NULL ,
                  `version` INT NULL ,
                  `info` TEXT NULL
                  PRIMARY KEY (`dirname`) )
                ENGINE = InnoDB
                DEFAULT CHARSET = utf8
        )

)

Array
(
    [database] => Array
        (
            [0] => CREATE  TABLE IF NOT EXISTS `menu_test` (
                              `mid` VARCHAR(150) NOT NULL ,
                              `menu_test` VARCHAR(45) NOT NULL ,
                              `name` VARCHAR(150) NOT NULL ,
                              PRIMARY KEY (`mid`, `language`) )
                            ENGINE = InnoDB
                            AUTO_INCREMENT = 1
                            DEFAULT CHARSET = utf8
        )

    [insert] => Array
        (
            [0] => Array
                (
                    [table] => menu_test
                    [fields] => Array
                        (
                            [mid] => menu_admin
                            [language] => EN
                            [name] => Admin
                        )

                )

            [1] => Array
                (
                    [table] => menu_test
                    [fields] => Array
                        (
                            [mid] => menu_seo
                            [language] => EN
                            [name] => Menu SEO
                        )

                )

$database = DOCUMENT_ROOT."sites/user/database.sql" ;
foreach ($schema as $type => $query)
        {
            switch ($type)
            {
                case "database"  :
                    foreach ($query as $sql)
                        file_put_contents($database,$sql.";");

                break ;
                case "insert"  :
                    foreach ($query as $sql)
                        file_put_contents($database,$sql.";");
                break ;
            }

        }

file_put_contents($database,$sql.";",FILE_APPEND); should work.