I would expect its something like one of the programs serving some aspect of the foundry may have crashed leading to some sort of cascade collapse of the entire system as the server got caught running loops when it couldn't find certain things. If there's a problem they should be able to fix it. The foundry is a big part of the game, and folks, remember its still technically in Beta! Soooo that means things like this can (and likely will from time to time) happen. They NEED to happen so that the devs can find the problems and fix them. Let them take their time to get things back up and running. In the meantime, do some STFs or grind lockboxes (if you are a sado-masochist), or better yet find some other way to spend your time while they get this fixed.
Thanks for your patience Captains! I've updated the OP with the following:
UPDATE #4 (9:08pm PDT): The Foundry for Star Trek Online is now available for use, including both the editing and playing of projects. If you see any irregularities with any of your missions (which you shouldn't), please send me a PM with your mission name, project code, and what's wrong. I will not be able to respond to PMs, but I will pass along the information to the team.