Added subfolder structure when copying

Hey, 
I saw the feature request for maintaining subfolder structure when uploading to s3.
I also had that need, along with the ability to base myself in a different working directory than the default workspace.

Here's my solution, for our needs.
I pretty heavily ripped apart the code base, since we needed this to be working quickly, so I dont expect this pull request to be merged, but I figured I'd share it with you anyway, in case you find any value in it.