Change the output structure in swift generator when using GitHub sync

I'm looking to change the output of the github sync with the swift 5 generator. Currently the structure contains code inside a file structure like `swift5/SwaggerClient/Classes/Swaggers`. It contains some content at the `swift5` level that I'm not interested in, such as Cartfile and Cocoapod files. My end goal here is to build a swift package managed repo which will only work if the code is in `Sources/<myPackageName>`. 

Question: Is there a way to move the root directory and not include any of the other dependency manager metadata?