I spent some time looking at the code, and I just need a little more understanding. If I'm understanding this correctly, the plugin registers a stream handler for s3:// and then changes the upload_dir to include the "s3" protocol. Subsequently the plugin then handles uploads with that protocol. Is that the gist of things? I ask because I want to be able to use the Easy Upload Files During Checkout plugin which writes to the local filesystem using wp_handle_upload which is dependent on the output of wp_upload_dir which you're mangling with the use of the upload_dir filter.

Did I get this right? Ultimately I want files uploaded to the site to be uploaded directly to S3 without hitting the local filesystem. Thanks.