We'll be releasing a tool to unpack the fmf files so that you can get access to the directory structure and files so it's not going to be a problem.
The main difference is that everything has to be added through the My Documents area (which everyone who followed our instructions for last versions should be doing anyway)
Not sure on the status of the tool. I've not even seen it myself but I'll be trying it out today and if it's fine then I'll be sending it to some of the people who have e-mailed me to test it out.
Please don't try to edit these files as it will most likely cause your game to either crash or not function.