Repair checkpoint-restart.

[tbenthompson]

In some of the latest work, I've disabled the checkpoint-restart functionality because I was rushing to get stuff done. This should be fixed in the long-term because it's very useful to be able to fix up a large job and restart it after something like a out-of-memory error.

There are a few tests of checkpoint-restart behavior in the tests/adagrid folder that are currently disabled.