Switch atomics to refs

[ericphanson]

Thanks to @vtjnash on #multithreading who pointed out the atomics don't do anything, because we aren't using atomic_not! to flip the boolean one, for example. He emphasized that atomics are relations, not objects, and it's the act of flipping the boolean that could be atomic (i.e. so you could get the current value and negate that, and then set that to be the value, all while knowing another thread hasn't changed the value inbetween getting and setting the value).

Here, however, we don't need to get and set together (atomically), we are just setting, so there is no need for an atomic (and it doesn't do anything).

I think we could use locks if we were concerned about multiple threads changing these values at once, but one just shouldn't do that (just choose the settings at the start of the script; doesn't really make sense to change it partway through a multithreaded computation). I don't think there's a problem with multiple threads reading the values at the same time.

This partially reverts #372 (i.e. reverts the atomic stuff, not the DCP warnings).