I should note that really everything but watching the file system for new QC files is already supported by SkylineRunner. So, you could just set up your own scheduled job to run at some interval, e.g. 1 hour or 30 minutes that would upload any files that were present. It just wouldn't automatically detect them the way AutoQC Loader does.
But we will look at making the waiting part automated so that you can just run it at the command-line without needing a scheduled task.