ENH: Allow template building to only do new files

It is desirable to simply skip sessions that are
completed so that the cluster is not bombarded with
unnecessary qsub jobs.
ENH: Add code for identifying the brain stem

This is an initial step toward robustly identifying the brain
stem from a set of images.
BUG: ATLAS_DIRECTORY to ATLAS_INSTALLING_DIRECTORY
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.