ACCUMULO-1854 Add helper method to extract AOF configuration entries
from a Configuration object.
ACCUMULO-1854 Add AIF test to retrieve relevant configuration entries.
Remove the internal AtomicIntegers in favor of state management through
the Configuration object.

Using static concurrent structures in the InputFormat didn't work well
when making multiple calls to the class and altering the state. By
holding state on the Configuration for the input format, we can
alleviate some of this and do better duplication checking.
ACCUMULO-1854 More unit tests and fix a bug.
ACCUMULO-1854 Make the same changes to AOF as AIF has.
ACCUMULO-1854 Lift duplicated code between AIF and AOF into a helper
class
ACCUMULO-1854 Ended up re-implementing some of the old approach to get
back to a functional state.

Couldn't solely use the Configuration for things as getting the same
Configuration each time getSplits is called isn't guaranteed. Since
getSplits are always called serially by one client, we can use that fact
to keep some state and not read the same data many times.