BUG: Fixed logic for set notation.

The logic for identifying jobs that need to be done
was not correct.
PERF: Fixed job submission logic to speed job start.

The SGE job submission criteria was too comples and was causing
the cluster manager to take too much time in submitting new
jobs that were ready to run.  This patch makes the defaults
simple to identify if they can run (i.e. specify only 1 thread
by default, rather than a range) so that the small jobs get
started quickly.
BUG: Add consistent use-sentinal file.

All three modes should use similar methods for specifying the sentinal files.