Checking in changes to the command-line interface with Matlab, Octave, and
SVDLIBC to fix a platform-based bug where the Process.waitFor() call does not
return because the associated input stream is not read.  Thanks for Fabian
Zehner for proposing the solution.
Fixed bug during calcuation of Assignments class where negative cluster indices
from CLUTO would cause IndexOutOfBounds exceptions.  The new behavior is to
exclude these un-clustered items from all cluster-based evaluations.  Added unit
tests to verify the code wasn't crashing any more.