Jenkins Continuous Integration with Amazon S3 - Everything is uploading to the root?

I'm running Jenkins and I have it successfully working with my GitHub account, but I can't get it working correctly with Amazon S3.

I installed the S3 plugin and when I run a build it successfully uploads to the S3 bucket I specify, but all of the files uploaded end up in the root of the bucket. I have a bunch of folders (such as /css /js and so on), but all of the files in those folders from hithub end up in the root of my S3 account.

Is it possible to get the S3 plugin to upload and retain the folder structure?