Call rsync with patterns instead a list of files in simple_upload

More detailed description [here](https://trello.com/card/add-directories-recursively-to-simple-upload-instead-of-creating-a-large-list-of-files-to-include/5049f6acdfae292e69e02a88/177). I've tested it using the test_transfer.py, examining the resulting rsync command. Seems to be OK, though it needs to be tested with a real run folder.