(got lost when I removed CONFIGURE_SUBMITTY.sh)

Do we need the "site" folder?
I suggest:
/var/local/submitty/logs/autograding
/var/local/submitty/logs/access
/var/local/submitty/logs/error

I'd say yes as just "error" or "access" is not clear what it might contain. Should it also contain errors from the autograder? How about errors from rainbow grades? Etc.

Unless we plan to start putting more component logs into these folders in which case then yes, we'd flatten the directory structure out a bit.

autograding & access are logs of normal activity at the system level. We might introduce other normal activity logs later. Autograding logs do contain some error messages within the log -- and I argue those specific errors should stay where they are.

The error log should be empty, if things are debugged and not malfunctioning. When things start malfunctioning, yes, I think all sorts of detailed errors could be written to that directory -- as a combined log or as separate files, whatever makes sense.

The autograding logs folder contains info allowing the sysadmin to monitor machine load. Instructors generally don't use this to debug. Rather they use the logs per assignment in their course directory.

The rainbow grades errors contain confidential info that should not be at the system level, but rather per course, so the instructor can get in there are tinker as needed.

@bmcutler So I've made the following changes to this:

1. flatten sites/* to be site_errors/ and access/
2. have CONFIGURE_SUBMITTY.py write out a JSON file with all answers
3. Have CONFIGURE_SUBMITTY.py supply the user with defaults with those defaults being the previously set configuration if file was loaded (so for rerunning CONFIGURE on the live server will just be hitting enter a bunch of times).

Once Travis finishes, I'm going to merge this, and we can address further concerns in new issues (like maybe add new flag to not even bother asking questions if the system already has the answers in the saved submitty_conf.json file).